U.S. patent application number 16/034134 was filed with the patent office on 2019-02-07 for bispecific single chain antibodies with specificity for high molecular weight target antigens.
The applicant listed for this patent is AMGEN RESEARCH (MUNICH) GMBH. Invention is credited to Claudia Blumel, Roman Kischel, Peter Kufer.
Application Number | 20190040133 16/034134 |
Document ID | / |
Family ID | 42073957 |
Filed Date | 2019-02-07 |
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United States Patent
Application |
20190040133 |
Kind Code |
A1 |
Kufer; Peter ; et
al. |
February 7, 2019 |
BISPECIFIC SINGLE CHAIN ANTIBODIES WITH SPECIFICITY FOR HIGH
MOLECULAR WEIGHT TARGET ANTIGENS
Abstract
The present invention provides a method for the selection of
bispecific single chain antibodies comprising a first binding
domain capable of binding to an epitope of CD3 and a second binding
domain capable of binding to the extracellular domain cell surface
antigens with a high molecular weight extracellular domain.
Moreover, the invention provides bispecific single chain antibodies
produced by the use of the method of the invention, nucleic acid
molecules encoding these antibodies, vectors comprising such
nucleic acid molecules and methods for the production of the
antibodies. Furthermore, the invention provides pharmaceutical
compositions comprising bispecific single chain antibodies of the
invention, medical uses of the same and methods for the treatment
of diseases comprising the administration of bispecific single
chain antibodies of the invention.
Inventors: |
Kufer; Peter; (Munich,
DE) ; Blumel; Claudia; (Munich, DE) ; Kischel;
Roman; (Munich, DE) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
AMGEN RESEARCH (MUNICH) GMBH |
Munich |
|
DE |
|
|
Family ID: |
42073957 |
Appl. No.: |
16/034134 |
Filed: |
July 12, 2018 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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14991189 |
Jan 8, 2016 |
10047159 |
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16034134 |
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13122271 |
Jul 14, 2011 |
9260522 |
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PCT/EP2009/062794 |
Oct 1, 2009 |
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14991189 |
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61101933 |
Oct 1, 2008 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
C07K 16/2863 20130101;
C07K 16/3069 20130101; C07K 16/2851 20130101; C07K 2317/31
20130101; C07K 2317/622 20130101; C12N 15/1037 20130101; A61K
39/39558 20130101; C07K 2317/732 20130101; A61P 35/00 20180101;
C07K 16/005 20130101; C07K 2317/34 20130101; C07K 16/2809 20130101;
A61K 2039/505 20130101; A61P 35/02 20180101 |
International
Class: |
C07K 16/28 20060101
C07K016/28; C12N 15/10 20060101 C12N015/10; C07K 16/30 20060101
C07K016/30; C07K 16/00 20060101 C07K016/00 |
Claims
1-17. (canceled)
18. A bispecific single chain antibody comprising a first domain
binding domain capable of binding to CD3 epsilon (CD3.epsilon.) of
human and non-chimpanzee primate and a second domain binding domain
capable of binding to (a) the extracellular domain of the mutated
human prostate-specific membrane antigen (PSMA) comprising the
amino acid sequence of SEQ ID NO: 447 but not to the extracellular
domain of the rodent PSMA; (b) the extracellular domain of the
mutated human fibroblast activation protein alpha (FAP.alpha.)
chimera comprising the amino acid sequence of SEQ ID NO: 448 but
not to the extracellular domain of the rodent FAP.alpha.; (c) the
four Ig domains (SEQ ID NO: 436), a cystein-rich domain (SEQ ID NO:
437), or the beta-chain of a sema domain (SEQ ID NO: 438) of the
extracellular domain of c-MET; (d) the mucin domain (SEQ ID NO:
440), the three EGF-like domains (SEQ ID NO: 441), or the
Sushi/SCR/CCP domain (SEQ ID NO: 442) of the extracellular domain
of TEM1; and (e) the three fibronectin type III domains (SEQ ID NO:
444), or the L2 domain (SEQ ID NO: 445) of the extracellular domain
of insulin-like growth factor 1 receptor (IGF-1R).
19. The bispecific single chain antibody of claim 18, wherein the
first domain capable of binding to an epitope of human and
non-chimpanzee primate CD3.epsilon. chain comprises an amino acid
sequence selected from the group consisting of SEQ ID NOs: 23, 25,
41, 43, 59, 61, 77, 79, 95, 97, 113, 115, 131, 133, 149, 151, 167,
169, 185 and 187.
20. The bispecific single chain antibody of claim 18, wherein the
second domain comprises a VL region comprising CDR-L1, CDR-L2 and
CDR-L3 selected from the group consisting of: (a) CDR-L1 as
depicted in SEQ ID NO. 269, CDR-L2 as depicted in SEQ ID NO: 270
and CDR-L3 as depicted in SEQ ID NO. 271; (b) CDR-L1 as depicted in
SEQ ID NO. 283, CDR-L2 as depicted in SEQ ID NO: 284 and CDR-L3 as
depicted in SEQ ID NO. 285; (c) CDR-L1 as depicted in SEQ ID NO.
297, CDR-L2 as depicted in SEQ ID NO: 298 and CDR-L3 as depicted in
SEQ ID NO. 299; (d) CDR-L1 as depicted in SEQ ID NO. 311, CDR-L2 as
depicted in SEQ ID NO: 312 and CDR-L3 as depicted in SEQ ID NO.
313; (e) CDR-L1 as depicted in SEQ ID NO. 325, CDR-L2 as depicted
in SEQ ID NO. 326 and CDR-L3 as depicted in SEQ ID NO. 327; (f)
CDR-L1 as depicted in SEQ ID NO. 255, CDR-L2 as depicted in SEQ ID
NO. 256 and CDR-L3 as depicted in SEQ ID NO. 257; and (g) CDR-L1 as
depicted in SEQ ID NO. 481, CDR-L2 as depicted in SEQ ID NO. 482
and CDR-L3 as depicted in SEQ ID NO. 483.
21. The bispecific single chain antibody of claim 18, wherein the
second domain comprises a VH region comprising CDR-H1, CDR-H2 and
CDR-H3 selected from the group consisting of: (a) CDR-H1 as
depicted in SEQ ID NO. 274, CDR-H2 as depicted in SEQ ID NO: 275
and CDR-H3 as depicted in SEQ ID NO. 276; (b) CDR-H1 as depicted in
SEQ ID NO. 288, CDR-H2 as depicted in SEQ ID NO: 289 and CDR-H3 as
depicted in SEQ ID NO. 290; (c) CDR-H1 as depicted in SEQ ID NO.
302, CDR-H2 as depicted in SEQ ID NO: 303 and CDR-H3 as depicted in
SEQ ID NO. 304; (d) CDR-H1 as depicted in SEQ ID NO. 316, CDR-H2 as
depicted in SEQ ID NO: 317 and CDR-H3 as depicted in SEQ ID NO.
318; (e) CDR-H1 as depicted in SEQ ID NO. 330, CDR-H2 as depicted
in SEQ ID NO: 331 and CDR-H3 as depicted in SEQ ID NO. 332; (f)
CDR-H1 as depicted in SEQ ID NO. 260, CDR-H2 as depicted in SEQ ID
NO: 261 and CDR-H3 as depicted in SEQ ID NO. 262; and (g) CDR-H1 as
depicted in SEQ ID NO. 476, CDR-H2 as depicted in SEQ ID NO: 477
and CDR-H3 as depicted in SEQ ID NO. 478.
22. The bispecific single chain antibody of claim 18, wherein the
second domain comprises a VL region and a VH region selected from
the group consisting of: (a) a VL region as depicted in SEQ ID NO.
268 and a VH region as depicted in SEQ ID NO. 273; (b) a VL region
as depicted in SEQ ID NO. 282 and a VH region as depicted in SEQ ID
NO. 287; (c) a VL region as depicted in SEQ ID NO. 296 and a VH
region as depicted in SEQ ID NO. 301; (d) a VL region as depicted
in SEQ ID NO. 310 and a VH region as depicted in SEQ ID NO. 315;
(e) a VL region as depicted in SEQ ID NO. 324 and a VH region as
depicted in SEQ ID NO. 329; (f) a VL region as depicted in SEQ ID
NO. 254 and a VH region as depicted in SEQ ID NO. 259; and (g) a VL
region as depicted in SEQ ID NO. 480 and a VH region as depicted in
SEQ ID NO. 475.
23. The bispecific single chain antibody of claim 18, wherein the
second domain comprises an amino acid sequence selected from the
group consisting of SEQ ID NOs: 278, 292, 306, 320, 334, 485 and
264.
24. The bispecific single chain antibody molecule of claim 23,
wherein the bispecific single chain antibody molecule comprises a
sequence selected from the group consisting of: (a) an amino acid
sequence as depicted in any of SEQ ID NOs: 280, 294, 308, 322, 336,
266 or 487; (b) an amino acid sequence encoded by a nucleic acid
sequence as depicted in any of SEQ ID NOs: 281, 295, 267, 309, 323,
337 or 488; and (c) an amino acid sequence at least 90% identical,
more preferred at least 95% identical, most preferred at least 96%
identical to the amino acid sequence of (a) or (b).
25. (canceled)
26. The bispecific single chain antibody molecule of claim 18,
wherein the bispecific single chain antibody molecule comprises a
group of the following sequences as CDR H1, CDR H2, CDR H3, CDR L1,
CDR L2 and CDR L3 in the second binding domain selected from the
group consisting of: a) CDR H1-3 of SEQ ID NO: -808-810 and CDR
L1-3 of SEQ ID NO: -813-815; b) CDR H1-3 of SEQ ID NO: 794-796 and
CDR L1-3 of SEQ ID NO: 799-801; c) CDR H1-3 of SEQ ID NO: 738-740
and CDR L1-3 of SEQ ID NO: 743-745; d) CDR H1-3 of SEQ ID NO:
752-754 and CDR L1-3 of SEQ ID NO: 757-759; e) CDR H1-3 of SEQ ID
NO: 822-824 and CDR L1-3 of SEQ ID NO: 827-829; f) CDR H1-3 of SEQ
ID NO: 766-768 and CDR L1-3 of SEQ ID NO: 771-773; and g) CDR H1-3
of SEQ ID NO: 780-782 and CDR L1-3 of SEQ ID NO: 785-787.
27. The bispecific single chain antibody molecule of claim 26,
wherein the bispecific single chain antibody molecule comprises a
sequence selected from the group consisting of: (a) an amino acid
sequence as depicted in any of SEQ ID NOs: 819, 805, 749, 763, 833,
777 or 791; (b) an amino acid sequence encoded by a nucleic acid
sequence as depicted in any of SEQ ID NOs: 820, 806, 750, 764, 834,
778 or 792; and (c) an amino acid sequence at least 90% identical,
more preferred at least 95% identical, most preferred at least 96%
identical to the amino acid sequence of (a) or (b).
28-29. (canceled)
30. The bispecific single chain antibody molecule of claim 18,
wherein the bispecific single chain antibody molecule comprises a
group of the following sequences as CDR H1, CDR H2, CDR H3, CDR L1,
CDR L2 and CDR L3 in the second binding domain selected from the
group consisting of: a) CDR H1-3 of SEQ ID NO: 500-502 and CDR L1-3
of SEQ ID NO: 1505-507; b) CDR H1-3 of SEQ ID NO: 514-516 and CDR
L1-3 of SEQ ID NO: 519-521; c) CDR H1-3 of SEQ ID NO: 528-530 and
CDR L1-3 of SEQ ID NO: 533-535; d) CDR H1-3 of SEQ ID NO: 542-544
and CDR L1-3 of SEQ ID NO: 547-549; e) CDR H1-3 of SEQ ID NO:
556-558 and CDR L1-3 of SEQ ID NO: 561-563; f) CDR H1-3 of SEQ ID
NO: 570-572 and CDR L1-3 of SEQ ID NO: 575-577; g) CDR H1-3 of SEQ
ID NO: 584-586 and CDR L1-3 of SEQ ID NO: 589-591; h) CDR H1-3 of
SEQ ID NO: 598-600 and CDR L1-3 of SEQ ID NO: 603-605; i) CDR H1-3
of SEQ ID NO: 612-614 and CDR L1-3 of SEQ ID NO: 617-619; j) CDR
H1-3 of SEQ ID NO: 626-628 and CDR L1-3 of SEQ ID NO: 631-633; k)
CDR H1-3 of SEQ ID NO: 640-642 and CDR L1-3 of SEQ ID NO: 645-647;
I) CDR H1-3 of SEQ ID NO: 654-656 and CDR L1-3 of SEQ ID NO:
659-661; m) CDR H1-3 of SEQ ID NO: 668-670 and CDR L1-3 of SEQ ID
NO: 673-675; n) CDR H1-3 of SEQ ID NO: 682-684 and CDR L1-3 of SEQ
ID NO: 687-689; o) CDR H1-3 of SEQ ID NO: 696-698 and CDR L1-3 of
SEQ ID NO: 701-703; p) CDR H1-3 of SEQ ID NO: 710-712 and CDR L1-3
of SEQ ID NO: 715-717; and q) CDR H1-3 of SEQ ID NO: 724-726 and
CDR L1-3 of SEQ ID NO: 729-731.
31. The bispecific single chain antibody molecule of claim 30,
wherein the bispecific single chain antibody molecule comprises a
sequence selected from the group consisting of: (a) an amino acid
sequence as depicted in SEQ ID NO: 511, 525, 539, 553, 567 or 581;
(b) an amino acid sequence encoded by a nucleic acid sequence as
depicted in SEQ ID NO: 512, 526, 540, 554, 568 or 582; and (c) an
amino acid sequence at least 90% identical, more preferred at least
95% identical, most preferred at least 96% identical to the amino
acid sequence of (a) or (b).
32-35. (canceled)
36. The bispecific single chain antibody molecule of claim 18,
wherein the bispecific single chain antibody molecule comprises a
group of the following sequences as CDR H1, CDR H2, CDR H3, CDR L1,
CDR L2 and CDR L3 in the second binding domain selected from the
group consisting of: a) CDR H1-3 of SEQ ID NO: 836-838 and CDR L1-3
of SEQ ID NO: 841-843; and b) CDR H1-3 of SEQ ID NO: 850-852 and
CDR L1-3 of SEQ ID NO: 855-857.
37. The bispecific single chain antibody molecule of claim 36,
wherein the bispecific single chain antibody molecule comprises a
sequence selected from the group consisting of: (a) the amino acid
sequence of SEQ ID NO: 847 or 861; (b) an amino acid sequence
encoded by the nucleic acid sequence of SEQ ID NO: 848 or 862; and
(c) an amino acid sequence at least 90% identical to the amino acid
sequence of (a) or (b).
38. (canceled)
39. A nucleic acid sequence encoding the bispecific single chain
antibody molecule of claim 18.
40. A vector comprising the nucleic acid sequence of claim 39.
41-42. (canceled)
43. A host transformed or transfected with the nucleic acid of
claim 39.
44. A process for producing a bispecific single chain antibody
molecule, said process comprising culturing the host of claim 43
under conditions allowing the expression of the the bispecific
single chain antibody molecule.
45. A composition comprising the bispecific single chain antibody
molecule of claim 18 and a pharmaceutically acceptable carrier.
46. (canceled)
47. A method for preventing, treating or ameliorating a cancer or
autoimmune disease comprising administering an effective amount of
the bispecific single chain antibody molecule of claim 18.
48-55. (canceled)
56. The method of claim 47, wherein said cancer is (a) a solid
tumor; (b) a carcinoma, sarcoma, glioblastoma/astrocytoma,
melanoma, mesothelioma, Wilms tumor or a hematopoietic malignancy
such as leukemia, lymphoma or multiple myeloma; (c) a
neuroectodermal tumor; (d) an epithelial cancer; or (e) a bone or
soft tissue cancer, or breast, liver, lung, head and neck,
colorectal, prostate, leiomyosarcoma, cervical and endometrial
cancer, ovarian, prostate, and pancreatic cancer.
57-61. (canceled)
Description
[0001] This application is a Divisional of U.S. application Ser.
No. 14/991,189, filed Jan. 8, 2016 (now U.S. Pat. No. 10,047,159),
which was a Divisional of U.S. application Ser. No. 13/122,271,
filed Jul. 14, 2011 (now U.S. Pat. No. 9,260,522, issued Feb. 16,
2016), which is the U.S. National Phase of International
Application No. PCT/EP2009/062794, filed Oct. 1, 2009, which claims
benefit of U.S. Provisional Patent Application No. 61/101,933,
filed Oct. 1, 2008, each of which is incorporated herein by
reference in its entirety.
[0002] The present invention provides a method for the selection of
bispecific single chain antibodies comprising a first binding
domain capable of binding to an epitope of CD3 and a second binding
domain capable of binding to to the extracellular domain cell
surface antigens with a high molecular weight extracellular domain.
Moreover, the invention provides bispecific single chain antibodies
produced by the use of the method of the invention, nucleic acid
molecules encoding these antibodies, vectors comprising such
nucleic acid molecules and methods for the production of the
antibodies. Furthermore, the invention provides pharmaceutical
compositions comprising bispecific single chain antibodies of the
invention, medical uses of the same and methods for the treatment
of diseases comprising the administration of bispecific single
chain antibodies of the invention.
[0003] Unifying two antigen binding sites of different specificity
into a single construct, bispecific antibodies have the ability to
bring together two discrete antigens with exquisite specificity and
therefore have great potential as therapeutic agents. This
potential was recognized early on, leading to a number of
approaches for obtaining such bispecific antibodies. Bispecific
antibodies were originally made by fusing two hybridomas, each
capable of producing a different immunoglobulin. The resulting
hybrid-hybridoma, or quadroma, was capable of producing antibodies
bearing the antigen specificity of the first parent hybridoma as
well as that of the second parent hybridoma (Milstein et al.,
(1983) Nature 305, 537). However, the antibodies resulting from
quadromas often exhibited undesired properties due to the presence
of an Fc antibody portion.
[0004] Largely due to such difficulties, attempts later focused on
creating antibody constructs resulting from joining two scFv
antibody fragments while omitting the Fc portion present in full
immunoglobulins. Each scFv unit in such constructs was made up of
one variable domain from each of the heavy (VH) and light (VL)
antibody chains, joined with one another via a synthetic
polypeptide linker, the latter often being genetically engineered
so as to be minimally immunogenic while remaining maximally
resistant to proteolysis. Respective scFv units were joined by a
number of techniques including incorporation of a short (usually
less than 10 amino acids) polypeptide spacer bridging the two scFv
units, thereby creating a bispecific single chain antibody. The
resulting bispecific single chain antibody is therefore a species
containing two VH/VL pairs of different specificity on a single
polypeptide chain, wherein the VH and VL domains in a respective
scFv unit are separated by a polypeptide linker long enough to
allow intramolecular association between these two domains, and
wherein the thusly formed scFv units are contiguously tethered to
one another through a polypeptide spacer kept short enough to
prevent unwanted association between, for example, the VH domain of
one scFv unit and the VL of the other scFv unit.
[0005] Bispecific single chain antibodies of the general form
described above have the advantage that the nucleotide sequence
encoding the four V-domains, two linkers and one spacer can be
incorporated into a suitable host expression organism under the
control of a single promoter. This increases the flexibility with
which these constructs can be designed as well as the degree of
experimenter control during their production.
[0006] Remarkable experimental results have been obtained using
such bispecific single chain antibodies designed for the treatment
of malignancies (Mack, J. Immunol. (1997) 158, 3965-70; Mack, PNAS
(1995) 92, 7021-5; Kufer, Cancer Immunol. Immunother. (1997) 45,
193-7; Loffler, Blood (2000) 95, 2098-103) and non-malignant
diseases (Bruhl, J. Immunol. (2001) 166, 2420-6); Brischwein et al.
J Immunother. (2007) 30(8), 798-807; Bargou, et al. (2008) Science
321, 974). If In such bispecific single chain antibodies, one scFv
unit is capable of activating cytotoxic cells, for example
cytotoxic T cells, within the immune system by specifically binding
to an antigen on the cytotoxic cells, while the other scFv unit
specifically binds an antigen on a malignant cell intended for
destruction. In this way, such bispecific single chain antibodies
have been shown to activate and redirect the immune system's
cytotoxic potential to the destruction of pathological, especially
malignant cells. In the absence of such a bispecific single chain
antibody construct, malignant cells would otherwise proliferate
uninhibited.
[0007] When designing a new bispecific single chain antibodies
comprising one scFv unit is capable of recruiting cytotoxic cells,
for example cytotoxic T cells, while the other scFv unit
specifically binds an antigen on a target cell to be eliminated by
the recruited cytotoxic cell, it has been observed that different
combination of scFv's in the bispecific single chain antibodies
show different effectively in the elimination of the target cells.
The election of a promising candidate is an intensive and time
consuming procedure.
[0008] The present invention provides means and methods for the
solution of this problem for a bispecific single chain antibodies
binding with one domain to cytotoxic cells, i.e. cytotoxic T cells,
and with the second binding domain to target antigens with a high
molecular weight extracellular domain.
[0009] Accordingly, the present invention provides in a first
embodiment a method for the selection of bispecific single chain
antibodies comprising a first binding domain capable of binding to
an epitope of CD3 and a second binding domain capable of binding to
the extracellular domain cell surface antigens with a high
molecular weight extracellular domain. Different binding domains,
which may be used as first binding domain, are described in the art
and in the appended sequence listing. As apparent from the above,
the election of an antigenic domain on a target cell for of
preparation of a target cell binding domain of a bispecific single
chain antibody is the critical step for the provision of new
bispecific single chain antibodies which allow for an efficient
elimination of target cells via redirected T cell lysis. A first
choice for the election of an antigenic domain on a target cell for
of preparation of a target cell binding domain of a bispecific
single chain antibody might be a domain, which is easily accessible
from a steric point of view. Accordingly, the person skilled in the
art would elect in the case cell surface proteins on target cells
with a high molecular weight extracellular domain epitopes which
are most distant from the target cell surface are most exposed,
therefore best accessible for T cells and thus particularly potent
in redirecting T cell cytotoxicity. However, it has been
surprisingly found that membrane distant epitopes of target cell
surface antigens with a high molecular weight extracellular domain
show a poor potency of redirecting T cell cytotoxicity.
[0010] The method of the invention provides guidance for the
election of antigenic regions of cell surface antigens with a high
molecular weight extracellular domain which allow for the selection
of bispecific single chain antibodies with a high potency for
redirected T cell cytotoxicity. These cell surface antigens with a
high molecular weight extracellular domain are type I or type II
integral membrane proteins with an extracellular portion of >640
amino acids. The extracellular portion of this group of membrane
proteins is independently folded, thus formed by a single
continuous stretch of extracellular amino acids adjacent to the
transmembrane region in the primary protein sequence. In order to
fulfil the requirement of a high molecular weight extracellular
domain in the context of the invention, the extracellular domain
essentially comprises more than 640 amino acids. Optionally the
extracellular domain is charcterized by at least one functionally
and/or structurally defined subdomain formed by discontinuous
stretches of extracellular amino acids within the primary protein
sequence. Examples for such cell surface antigens comprise
prostate-specific membrane antigen (PSMA), fibroblast activation
protein .alpha. (FAP.alpha.), Hepatocyte Growth Factor Receptor
(c-MET), endosialin (TEM1 or CD248) and type 1 insulin-like growth
factor receptor (IGF-1R).
[0011] PSMA and FAP.alpha. are cell surface molecules for which the
crystal structure and, thus, the three dimensional structure of the
extracellular domain are known in the art. These antigens show a
compact discontinuous domain composition of the extracellular
domain. It has been surprisingly found that bispecific single chain
antibodies binding to epitopes with a distance of up to 60 .ANG.
from the alpha C-atom of the thirteenth extracellular amino acid as
counted from the junction of transmembrane and extracellular region
(reference C-atom) show a significant high efficiency in the
redirected T cell lysis of target cells. In contrast thereto, the
efficiency in the redirected T cell lysis of target cells of
bispecific single chain antibodies binding only to epitopes with a
distance of more than 60 .ANG. from the reference C-atom is reduced
and thus renders such bispecific antibodies unattractive for a
clinical development.
[0012] c-MET, TEM1 and IGF-1R are are cell surface molecules having
a consecutive sequence of independently folded extracellular
domains is formed by a corresponding sequence of continuous
stretches of extracellular amino acids within the primary protein
sequence. It has been surprisingly found that bispecific single
chain antibodies binding to epitopes within the first 640 amino
acid residues counted from the junction of transmembrane and
extracellular region show a significant high efficiency in the
redirected T cell lysis of target cells. In contrast thereto, the
efficiency in the redirected T cell lysis of target cells of
bispecific single chain antibodies binding only to epitopes within
the amino acid recidues above the 640.sup.th amino acid residue
counted from the junction of transmembrane and extracellular region
is reduced and thus renders such bispecific antibodies unattractive
for a clinical development.
[0013] Based on these findings the invention relates in one
embodiment to a method for the selection of bispecific single chain
antibodies comprising a first binding domain capable of binding to
an epitope of CD3 and a second binding domain capable of binding to
the extracellular domain of prostate-specific membrane antigen
(PSMA), the method comprising the steps of: [0014] (a) providing at
least three types of host cells expressing [0015] (i) the wt human
extracellular domain of PSMA (SEQ ID NO: 447) on the cell surface;
[0016] (ii) a mutated form of the wt human PSMA on the cell
surface, wherein the amino acid residues at positions 140, 169,
191, 308, 334, 339, 344, 624, 626, 716, 717 and 721 are mutated to
the corresponding amino acid residues of the wt rodent PSMA; and
[0017] (iii) the rodent wt extracellular domain of PSMA on the cell
surface; [0018] (b) contacting each type of host cells (i), (ii)
and (iii) of step (a) with the bispecific single chain antibodies
and effector T cells; and [0019] (c) identifying and isolating the
bispecific single chain antibodies that mediate the lysis of host
cells expressing wt human extracellular domain of PSMA on the cell
surface according to (b)(i) and of host cells expressing mutated
form of the wt human PSMA on the cell surface according to (b)(ii)
but not of host cells expressing the rodent wt extracellular domain
of PSMA on the cell surface according to b(iii).
[0020] As noted above, prostate-specific membrane antigen (PSMA;
PSM) is a large antigen falling under the provided definition of
cell surface antigens with a high molecular weight extracellular
domai. Israeli et al. (Cancer Res. 53: 227-230, 1993) cloned a
2.65-kb cDNA for a prostate-specific membrane antigen detected with
a monoclonal antibody raised against the human prostatic carcinoma
cell line LNCaP. The PSMA gene encodes a 750-amino acid protein
that has an apparent molecular weight of 100 kD (due to
posttranslational modification) and is expressed by normal and
neoplastic prostate cells. PSMA was originally defined by the
monoclonal antibody (MAb) 7E11 derived from immunization with a
partially purified membrane preparation from the lymph node
prostatic adenocarcinoma (LNCaP) cell line (Horoszewicz et al.,
Anticancer Res. 7 (1987), 927-35). A 2.65-kb cDNA fragment encoding
the PSMA protein was cloned and subsequently mapped to chromosome
11p11.2 (Israeli et al., loc. cit.; O'Keefe et al., Biochem.
Biophys. Acta 1443 (1998), 113-127). Initial analysis of PSMA
demonstrated widespread expression within the cells of the
prostatic secretory epithelium. Immunohistochemical staining
demonstrated that PSMA was absent to moderately expressed in
hyperplastic and benign tissues, while malignant tissues stained
with the greatest intensity (Horoszewicz et al., loc. cit.).
Subsequent investigations have recapitulated these results and
evinced PSMA expression as a universal feature in practically every
prostatic tissue examined to date. These reports further
demonstrate that expression of PSMA increases precipitously
proportional to tumor aggressiveness (Burger et al., Int. J. Cancer
100 (2002), 228-237; Chang et al., Cancer Res. 59 (1999), 3192-98;
Chang et al., Urology 57 (2001), 1179-83), Kawakami and Nakayama,
Cancer Res. 57 (1997), 2321-24; Liu et al., Cancer Res. 57 (1997),
3629-34; Lopes et al., Cancer Res. 50 (1990), 6423-29; Silver et
al., Clin. Cancer Res. 9 (2003), 6357-62; Sweat et al., Urology 52
(1998), 637-40; Troyer et al., Int. J. Cancer 62 (1995), 552-558;
Wright et al., Urology 48 (1996), 326-334). Consistent with the
correlation between PSMA expression and tumor stage, increased
levels of PSMA are associated with androgen-independent prostate
cancer (PCa). Analysis of tissue samples from patients with
prostate cancer has demonstrated elevated PSMA levels after
physical castration or androgen-deprivation therapy. Unlike
expression of prostate specific antigen, which is downregulated
after androgen ablation, PSMA expression is significantly increased
in both primary and metastatic tumor specimens (Kawakami et al.,
Wright et al., loc. cit.). Consistent with the elevated expression
in androgen-independent tumors, PSMA transcription is also known to
be downregulated by steroids, and administration of testosterone
mediates a dramatic reduction in PSMA protein and mRNA levels
(Israeli et al., Cancer Res. 54 (1994), 1807-11; Wright et al.,
loc. cit.). PSMA is also highly expressed in secondary prostatic
tumors and occult metastatic disease. Immunohistochemical analysis
has revealed relatively intense and homogeneous expression of PSMA
within metastatic lesions localized to lymph nodes, bone, soft
tissue, and lungs compared with benign prostatic tissues (Chang et
al. (2001), loc. cit.; Murphy et al., Cancer 78 (1996), 809-818;
Sweat et al., loc. cit.). Some reports have also indicated limited
PSMA expression in extraprostatic tissues, including a subset of
renal proximal tubules, some cells of the intestinal brush-border
membrane, and rare cells in the colonic crypts (Chang et al.
(1999), Horoszewicz et al., Israeli et al. (1994), Lopes et al.,
Troyer et al., loc. cit.). However, the levels of PSMA in these
tissues are generally two to three orders of magnitude less than
those observed in the prostate (Sokoloff et al., Prostate 43
(2000), 150-157). PSMA is also expressed in the tumor-associated
neovasculature of most solid cancers examined yet is absent in the
normal vascular endothelium (Chang et al. (1999), Liu et al.,
Silver et al., loc. cit.). Although the significance of PSMA
expression within the vasculature is unknown, the specificity for
tumor-associated endothelium makes PSMA a potential target for the
treatment of many forms of malignancy.
[0021] As apparent from SEQ ID NO: 447 the extracellular domain of
PSMA comprises 707 amino acid residues. The 13.sup.th aa as counted
from the junction of transmembrane and extracellular region
(reference C-atom) is a histidine. The identification of the amino
acid residues to be mutated for the mutant human PSMA is described
in detail in appended example 2. According to the method of the
invention all amino acid residues which do not match between the
mouse and the rodent extracellular domain of PSMA and which have a
distance of more than 60 .ANG. from the reference C-atom are
mutatet from the human sequence to the rodent sequence. This
mutation results in a transformation of all antigenic regions with
a distance of more than 60 .ANG. from the reference C-atom from the
human specific form to the rodent specific form. Antibodies, e.g.
bispecific antibodies which are specific for human epitopes
comprising antigenic regions with a distance of more than 60 .ANG.
from the reference C-atom (specific for membrane distal epitopes)
do not bind to the mutant human PSMA and the rodent PSMA.
Accordingly, the method of the invention allows for a
discrimination of antibodies which bind to epitopes comprising
antigenic regions with a distance of more than 60 .ANG. from the
reference C-atom (antibodies specific for membrane distal epitopes)
and a positive identification and isolation of antibodies specific
for epitopes of the human PSMA within a distance of less than 60
.ANG. from the reference C-atom (antibodies specific for membrane
proximal epitopes).
[0022] As apparent from the appended examples it has been
surprisingly observed that the distance of the epitope from the
cell membrane is a critical factor for the cytotoxic potency of a
bispecific single chain antibody which engages effector T cells and
target cells, such as PSMA cells. The general effect underlying the
distance between the epitope, which is bound by an according
bispecific single chain antibody, from the cell membrane of a
target cell is exemplified in a model in the appended example 1.
What came as a surprise according to this example, however, was the
large extent of the loss in target cell lysis observed between a
target size of 640 aa (D1) and 679 aa (D3). Despite this small
difference in target size there was more loss in target cell lysis
than from 679 aa (D3) to 1319 aa (D1+D3). Thus, a target size of
640 aa was unexpectedly found as upper threshold for the
membrane-distant epitopes of bispecific single chain antibodies,
still capable of inducing redirected T cell cytotoxicity with
reasonable potency without requiring compensation for the negative
influence of more membrane-distance by other properties of the
bscAb such as a very high affinity to the target antigen. Moreover,
the cytotxic potency relative to the distance of the epitope bound
by a bispecific single chain antibody is demonstrated in examples 3
and 4.
[0023] Examples for assays for performing the steps of the method
according to the invention are described in the appended
examples.
[0024] The invention further relates to a method for the selection
of bispecific single chain antibodies comprising a first binding
domain capable of binding to an epitope of CD3 and a second binding
domain capable of binding to the extracellular domain of fibroblast
activation protein .alpha. (FAP.alpha.), the method comprising the
steps of: [0025] (a) providing at least three types of host cells
expressing [0026] (i) the wt human extracellular domain of
FAP.alpha. (SEQ ID NO: 448) on the cell surface; [0027] (ii) a
mutated form of the wt human FAP.alpha. on the cell surface,
wherein the amino acid residues at positions 144, 185, 186, 229,
267, 273, 274, 278, 284, 301, 328, 329, 331, 335 and 362 are
mutated to the corresponding amino acid residues of the wt rodent
FAP.alpha.; and [0028] (iii) the rodent wt extracellular domain of
FAP.alpha. on the cell surface; [0029] (b) contacting each type of
host cells (i), (ii) and (iii) of step (a) with the bispecific
single chain antibodies and effector T cells; and [0030] (c)
identifying and isolating the bispecific single chain antibodies
that mediate the lysis of host cells expressing wt human
extracellular domain of FAP.alpha. on the cell surface according to
(b)(i) and of host cells expressing mutated form of the wt human
FAP.alpha. on the cell surface according to (b)(ii) but not of host
cells expressing the rodent wt extracellular domain of FAP.alpha.
on the cell surface according to b(iii).
[0031] Another large antigen according to the above definition is
the cell surface protease fibroblast activation protein alpha (FAP
alpha). In epithelial cancer, invasion and metastasis of malignant
epithelial cells into normal tissues is accompanied by adaptive
changes in the mesenchyme-derived supporting stroma of the target
organs. Altered gene expression in these non-transformed stromal
cells has been discussed to provide potential targets for therapy.
FAP alpha is such an example for a target of activated tumor
fibroblasts in tumor stroma. Fibroblast activation protein alpha is
an inducible cell surface glycoprotein that has originally been
identified in cultured fibroblasts using monoclonal antibody F19.
Immunohistochemical studies have shown that FAP alpha is
transiently expressed in certain normal fetal mesenchymal tissues
but that normal adult tissues as well as malignant epithelial,
neural, and hematopoietic cells are generally FAP alpha-negative.
However, most of the common types of epithelial cancers contain
abundant FAP alpha-reactive stromal fibroblasts. FAP alpha cDNA was
cloned and published in GenBank (Accession number NM_004460). The
predicted human FAP alpha protein is a type II integral membrane
protein with a large C-terminal extracellular domain, which
contains 6 potential N-glycosylation sites, 13 cysteine residues,
and 3 segments that correspond to highly conserved catalytic
domains of serine proteases; a hydrophobic transmembrane segment;
and a short cytoplasmic tail. FAP-alpha shows 48% amino acid
identity with dipeptidyl peptidase IV (DPP4) and 30% identity with
DPP4-related protein (DPPX). Northern blot analysis detected a
2.8-kb FAP alpha mRNA in fibroblasts. Seprase is a 170-kD integral
membrane gelatinase whose expression correlates with the
invasiveness of human melanoma and carcinoma cells. Goldstein et
al. (Biochim. Biophys. Acta 1361: 11-19, 1997) cloned and
characterized the corresponding seprase cDNA. The authors found
that seprase and FAP alpha are the same protein and products of the
same gene. Pineiro-Sanchez et al. (J. Biol. Chem. 272: 7595-7601,
1997) isolated seprase/FAP alpha protein from the cell membranes
and shed vesicles of human melanoma LOX cells. Serine protease
inhibitors blocked the gelatinase activity of seprase/FAP alpha,
suggesting that seprase/FAP alpha contains a catalytically active
serine residue(s). The authors found that seprase/FAP alpha is
composed of monomeric, N-glycosylated 97-kD subunits that are
proteolytically inactive. They concluded that seprase/FAP alpha is
similar to DPP4 in that their proteolytic activities are dependent
upon subunit association. Due to its degrading activity of gelatine
and heat-denatured type-I and type-IV collagen, a role for
seprase/FAP alpha in extracellular matrix remodeling, tumor growth,
and metastasis of cancers has been suggested. Moreover, seprase/FAP
alpha shows a restricted expression pattern in normal tissues and a
uniform expression in the supporting stroma of many malignant
tumors. Therefore, seprase/FAP alpha may be used as a target for
exploring the concept of tumor stroma targeting for immunotherapy
of human epithelial cancer. However, though several clinical trials
have been initiated to investigate seprase's/FAP alpha's role as a
tumor antigen target, conventional immunotherapy approaches or
inhibition of seprase/FAP alpha enzymatic activity so far did not
yet result in therapeutic efficacy (see e.g. Welt et al., J. Clin.
Oncol. 12:1193-203, 1994; Narra et al., Cancer Biol. Ther. 6,
1691-9, 2007; Henry et al., Clinical Cancer Research 13, 1736-1741,
2007). As apparent from SEQ ID NO: 448 the extracellular domain of
FAP.alpha. comprises 734 amino acid residues. The 13.sup.th aa as
counted from the junction of transmembrane and extracellular region
(reference C-atom) is a methionine. The identification of the amino
acid residues to be mutated for the mutant human FAP.alpha. is
described in detail in appended example 5. According to the method
of the invention all amino acid residues which do not match between
the mouse and the rodent extracellular domain of FAP.alpha. and
which have a distance of more than 60 .ANG. from the reference
C-atom are mutatet from the human sequence to the rodent
sequence.
[0032] Moreover, the invention relates to a method for the
selection of bispecific single chain antibodies comprising a first
binding domain capable of binding to an epitope of CD3 and a second
binding domain capable of binding to the extracellular domain of
Hepatocyte Growth Factor Receptor (c-MET), endosialin (TEM1) and
type 1 insulin-like growth factor receptor (IGF-1R), the method
comprising the steps of: [0033] (a) identifying the membrane
proximal 640 amino acid residues of the human and the rodent
homolog of the extracellular domain of c-MET, TEM1 or IGF-1R;
[0034] (b) providing host cells expressing [0035] (i) the human wt
of the extracellular domain of the extracellular domain of c-MET
(SEQ ID NO: 439), TEM1 (SEQ ID NO: 443) or IGF-1R (SEQ ID NO: 446)
on the cell surface; [0036] (ii) a fusion protein comprising the
human membrane proximal 640 amino acid residues identified in step
(a) and the rodent amino acid residues >640 of c-MET, TEM1 or
IGF-1R; and [0037] (iii) the rodent wt extracellular domain of
c-MET, TEM1 or IGF-1R; [0038] (c) contacting the host cells
according to step (b) with the bispecific single chain antibodies
and effector T cells; and [0039] (d) identifying and isolating the
bispecific single chain antibodies that mediate the lysis of host
cells according to (b)(i) and (b)(ii) but not of host cells
according to b(iii).
[0040] As described herein above, c-MET, TEM1 and IGF-1R are type I
or type II integral membrane proteins with an extracellular portion
of more than 640 amino acids. The consecutive sequence of the
extracellular domain comprises continuous stretches of
extracellular amino acids within the primary protein sequence and
independently folded extracellular subdomain formed by a single
continuous stretches. Hepatocyte growth factor receptor MET (C-MET)
is involved in the progression and spread of numerous human cancer
types. The MET oncogene, encoding the receptor tyrosin kinase (RTK)
for hepatocyte growth factor (HGF) and Scatter Factor (SF),
controls genetic programs leading to cell growth, invasion, and
protection from apoptosis. Deregulated activation of MET is
critical not only for the acquisition of tumorigenic properties but
also for the achievement of the invasive phenotype (Trusolino, L.
& Comoglio, P. M. (2002) Nat. Rev. Cancer 2, 289-300). The role
of MET in human tumors emerged from several experimental approaches
and was unequivocally proven by the discovery of MET-activating
mutations in inherited forms of carcinomas (Schmidt et al., Nat.
Genet. 16 (1997), 68-73; Kim et al., J. Med. Genet. 40 (2003),
e97). MET constitutive activation is frequent in sporadic cancers,
and several studies have shown that the MET oncogene is
overexpressed in tumors of specific histotypes or is activated
through autocrine mechanisms (for a list see
http://www.vai.org/met/). Besides, the MET gene is amplified in
hematogenous metastases of colorectal carcinomas (Di Renzo et al.,
Clin. Cancer Res. 1 (1995), 147-154). The Scatter Factor (SF)
secreted in culture by fibroblasts, that have the ability to induce
intercellular dissociation of epithelial cells, and the Hepatocyte
Growth Factor (HGF), a potent mitogen for hepatocytes in culture
derived from platelets or from blood of patients with acute liver
failure, independently identified as Met ligands turned out to be
the same molecule. Met and SF/HGF are widely expressed in a variety
of tissues. The expression of Met (the receptor) is normally
confined to cells of epithelial origin, while the expression of
SF/HGF (the ligand) is restricted to cells of mesenchymal origin.
Met is a transmembrane protein produced as a single-chain
precursor. The precursor is proteolytically cleaved at a furin site
to produce a highly glycosylated and entirely extracellular
.alpha.-subunit of 50 kd and a .beta.-subunit of 145 kd with a
large extracellular region (involved in binding the ligand), a
membrane spanning segment, and an intracellular region (containing
the catalytic activity) (Giordano (1989) 339: 155-156). The .alpha.
and .beta. chains are disulphide linked. The extracellular portion
of Met contains a region of homology to semaphorins (Sema domain,
which includes the full .alpha. chain and the N-terminal part of
the .beta. chain of Met), a cysteine-rich Met Related Sequence
(MRS) followed by glycineproline-rich (G-P) repeats, and four
Immunoglobuline-like structures (Birchmeier et al., Nature Rev. 4
(2003), 915-25). The intracellular region of Met contains three
regions: (1) a juxtamembrane segment that contains: (a) a serine
residue (Ser 985) that, when phosphorylated by protein kinase C or
by Ca.sup.2+calmodulin-dependent kinases downregulates the receptor
kinase activity Gandino et al., J. Biol. Chem. 269 (1994),
1815-20); and (b) a tyrosine (Tyr 1003) that binds the ubiquitin
ligase Cbl responsible for Met polyubiquitination, endocytosis and
degradation (Peschard et al., Mol. Cell 8 (2001), 995-1004); (2)
the tyrosine kinase domain that, upon receptor activation,
undergoes transphosphorylation on Tyr1234 and Tyr1235; (3) the
C-terminal region, which comprises two crucial tyrosines (Tyr1349
and Tyr1356) inserted in a degenerate motif that represents a
multisubstrate docking site capable of recruiting several
downstream adaptors containing Src homology-2 (SH2) domains Met
receptor, as most Receptor Tyrosine Kinases (RTKs) use different
tyrosines to bind specific signaling molecules. The two tyrosines
of the docking sites have been demonstrated to be necessary and
sufficient for the signal transduction both in vitro and in vivo
(Maina et al., Cell 87 (1996), 531-542; Ponzetto et aL, Cell 77
(1994), 261-71).
[0041] A further example for a molecule having a large
extracellular domain is the tumor endothelial marker (TEM)
Endosialin (=TEM1). TEMs are overexpressed during tumor
angiogenesis (St. Croix et al., Science 289 (2000), 1197-1202).
Despite the fact that their functions have not been characterized
in detail so far, it is well established that they are strongly
expressed on vascular endothelial cells in developing embryos and
tumors studies (Carson-Walter et al., Cancer Res. 61: 6649-6655,
2001). Accordingly, Endosialin, a 165-kDa type I transmembrane
protein, is expressed on the cell surface of tumor blood vessel
endothelium in a broad range of human cancers but not detected in
blood vessels or other cell types in many normal tissues. It is a
C-type lectin-like molecule of 757 amino acids composed of a signal
leader peptide, five globular extracellular domains (including a
C-type lectin domain, one domain with similarity to the
Sushi/ccp/scr pattern, and three EGF repeats), followed by a mucin
like region, a transmembrane segment, and a short cytoplasmic tail
(Christian et al., J. Biol. Chem. 276: 7408-7414, 2001). The
Endosialin core protein carries abundantly sialylated, O-linked
oligosaccharides and is sensitive to O-sialoglycoprotein
endopeptidase, placing it in the group of sialomucin-like
molecules. The N-terminal 360 amino acids of Endosialin show
homology to thrombomodulin, a receptor involved in regulating blood
coagulation, and to complement receptor C1qRp. This structural
relationship indicates a function for Endosialin as a tumor
endothelial receptor. Although Endosialin mRNA is ubiquitously
expressed on endothelial cells in normal human and murine somatic
tissues, Endosialin protein is largely restricted to the corpus
luteum and highly angiogenic tissues such as the granular tissue of
healing wounds or tumors (Opaysky et al., J. Biol. Chem. 276 (2001,
38795-38807; Rettig et al., PNAS 89 (1992), 10832-36). Endosialin
protein expression is upregulated on tumor endothelial cells of
carcinomas (breast, kidney, lung, colorectal, colon, pancreas
mesothelioma), sarcomas, and neuroectodermal tumors (melanoma,
glioma, neuroblastoma) (Rettig et al., loc. cit.). In addition,
Endosialin is expressed at a low level on a subset of tumor stroma
fibroblasts (Brady et al., J. Neuropathol. Exp. Neurol. 63 (2004),
1274-83; Opaysky et al., loc. cit.). Because of its restricted
normal tissue distribution and abundant expression on tumor
endothelial cells of many different types of solid tumors,
Endosialin has been discussed as a target for antibody-based
antiangiogenic treatment strategies of cancer. However, so far,
there are no effective therapeutic approaches using Endosialin as a
tumor endothelial target.
[0042] A still further example for a large antigen is the
insulin-like growth factor I receptor (IGF-IR or IGF-1R). IGF-IR is
a receptor with tyrosine kinase activity having 70% homology with
the insulin receptor IR. IGF-IR is a glycoprotein of molecular
weight approximately 350,000. It is a hetero-tetrameric receptor of
which each half-linked by disulfide bridges-is composed of an
extracellular .alpha.-subunit and of a transmembrane
[beta]-subunit. IGF-IR binds IGF I and IGF II with a very high
affinity but is equally capable of binding to insulin with an
affinity 100 to 1000 times less. Conversely, the IR binds insulin
with a very high affinity although the ICFs only bind to the
insulin receptor with a 100 times lower affinity. The tyrosine
kinase domain of IGF-IR and of IR has a very high sequence homology
although the zones of weaker homology respectively concern the
cysteine-rich region situated on the alpha-subunit and the
C-terminal part of the [beta]-subunit. The sequence differences
observed in the a-subunit are situated in the binding zone of the
ligands and are therefore at the origin of the relative affinities
of IGF-IR and of IR for the IGFs and insulin respectively. The
differences in the C-terminal part of the [beta]-subunit result in
a divergence in the signalling pathways of the two receptors;
IGF-IR mediating mitogenic, differentiation and antiapoptosis
effects, while the activation of the IR principally involves
effects at the level of the metabolic pathways (Baserga et al.,
Biochim. Biophys. Acta, 1332: F105-126, 1997; Baserga R., Exp.
Cell. Res., 253:1-6, 1999). The cytoplasmic tyrosine kinase
proteins are activated by the binding of the ligand to the
extracellular domain of the receptor. The activation of the kinases
in its turn involves the stimulation of different intra-cellular
substrates, including IRS-1, IRS-2, Shc and Grb 10 (Peruzzi F. et
al., J. Cancer Res. Clin. Oncol., 125:166-173, 1999). The two major
substrates of IGF-IR are IRS and Shc which mediate, by the
activation of numerous effectors downstream, the majority of the
growth and differentiation effects connected with the attachment of
the IGFs to this receptor. The availability of substrates can
consequently dictate the final biological effect connected with the
activation of the IGF-IR. When IRS-1 predominates, the cells tend
to proliferate and to transform. When Shc dominates, the cells tend
to differentiate (Valentinis B. et al.; J. Biol. Chem.
274:12423-12430, 1999). It seems that the route principally
involved for the effects of protection against apoptosis is the
phosphatidyl-inositol 3-kinases (PI 3-kinases) route (Prisco M. et
al., Horm. Metab. Res., 31:80-89, 1999; Peruzzi F. et al., J.
Cancer Res. Clin. Oncol., 125:166-173, 1999). The role of the IGF
system in carcinogenesis has become the subject of intensive
research in the last ten years. This interest followed the
discovery of the fact that in addition to its mitogenic and
antiapoptosis properties, IGF-IR seems to be required for the
establishment and the maintenance of a transformed phenotype. In
fact, it has been well established that an overexpression or a
constitutive activation of IGF-IR leads, in a great variety of
cells, to a growth of the cells independent of the support in media
devoid of fetal calf serum, and to the formation of tumors in nude
mice. This in itself is not a unique property since a great variety
of products of overexpressed genes can transform cells, including a
good number of receptors of growth factors. However, the crucial
discovery which has clearly demonstrated the major role played by,
IGF-IR in the transformation has been the demonstration that the
R-cells, in which the gene coding for IGF-IR has been inactivated,
are totally refractory to transformation by different agents which
are usually capable of transforming the cells, such as the E5
protein of bovine papilloma virus, an overexpression of EGFR or of
PDGFR, the T antigen of SV 40, activated ras or the combination of
these two last factors (Sell C. et al., Proc. Natl. Acad. Sci.,
USA, 90: 11217-11221, 1993; Sell C. et al., Mol. Cell. Biol.,
14:3604-3612, 1994; Morrione A. J., Virol., 69:5300-5303, 1995;
Coppola D. et al., Mol. Cell. Biol., 14:458a-4595, 1994; DeAngelis
T et al., J. Cell. Physiol., 164:214-221, 1995). IGF-IR is
expressed in a great variety of tumors and of tumor lines and the
IGFs amplify the tumor growth via their attachment to IGF-IR. Other
arguments in favor of the role of IGF-IR in carcinogenesis come
from studies using murine monoclonal antibodies directed against
the receptor or using negative dominants of IGF-IR. In effect,
murine monoclonal antibodies directed against IGF-IR inhibit the
proliferation of numerous cell lines in culture and the growth of
tumor cells in vivo (Arteaga C. et al., Cancer Res., 49:6237-6241,
1989 Li et al., Biochem. Biophys. Res. Com., 196:92-98, 1993; Zia F
et al., J. Cell. Biol., 24:269-275, 1996; Scotlandi K et al.,
Cancer Res., 58:4127-4131, 1998). It has likewise been shown in the
works of Jiang et al. (Oncogene, 18:6071-6077, 1999) that a
negative dominant of IGF-IR is capable of inhibiting tumor
proliferation.
[0043] The term "cell surface antigen" as used herein denotes a
molecule, which is displayed on the surface of a cell. In most
cases, this molecule will be located in or on the plasma membrane
of the cell such that at least part of this molecule remains
accessible from outside the cell in tertiary form. A non-limiting
example of a cell surface molecule, which is located in the plasma
membrane is a transmembrane protein comprising, in its tertiary
conformation, regions of hydrophilicity and hydrophobicity. Here,
at least one hydrophobic region allows the cell surface molecule to
be embedded, or inserted in the hydrophobic plasma membrane of the
cell while the hydrophilic regions extend on either side of the
plasma membrane into the cytoplasm and extracellular space,
respectively. Non-limiting examples of cell surface molecules which
are located on the plasma membrane are proteins which have been
modified at a cysteine residue to bear a palmitoyl group, proteins
modified at a C-terminal cysteine residue to bear a farnesyl group
or proteins which have been modified at the C-terminus to bear a
glycosyl phosphatidyl inositol ("GPI") anchor. These groups allow
covalent attachment of proteins to the outer surface of the plasma
membrane, where they remain accessible for recognition by
extracellular molecules such as antibodies. Examples of cell
surface antigens are CD3 (in particular CD3.epsilon.), PSMA,
FAP.alpha., c-MET, endosialin and IGF-IR. As described herein
above, PSMA, FAP.alpha., c-MET, endosialin and IGF-IR are cell
surface antigens which are targets for therapy of cancer,
including, but not limited to solid tumors.
[0044] In light of this, the target antigens PSMA, FAP.alpha.,
c-MET, endosialin and IGF-IR can also be characterized as tumor
antigens. The term "tumor antigen" as used herein may be understood
as those antigens that are presented on tumor cells. These antigens
can be presented on the cell surface with an extracellular part,
which is often combined with a transmembrane and cytoplasmic part
of the molecule. These antigens can sometimes be presented only by
tumor cells and never by the normal ones. Tumor antigens can be
exclusively expressed on tumor cells or might represent a tumor
specific mutation compared to normal cells. In this case, they are
called tumor-specific antigens. More common are antigens that are
presented by tumor cells and normal cells, and they are called
tumor-associated antigens. These tumor-associated antigens can be
overexpressed compared to normal cells or are accessible for
antibody binding in tumor cells due to the less compact structure
of the tumor tissue compared to normal tissue.
[0045] In accordance with the present invention an independently
folded protein domain is defined as a discrete portion of a protein
formed by a single continuous stretch of amino acids within the
primary protein sequence, e.g. known from its crystal structure, to
take the "correct conformation" without requiring support by other
portions of the protein or predicted to do so by comparison with
hidden Markow models in libraries of described sequence domains,
such as PFAM (Bateman (2000) Nucleic Acids Res. 28: 263-266) and
SMART (Schultz (2000) Nucleic Acids Res. 28: 231-234), sequence
similarity searches in data bases with the BLAST and PSI-BLAST
tools (Altschul (1997) Nucleic Acids Res. 25: 3389-3402) that rely
on the concept of a common evolutionary ancestor among sequentially
homologous sequences or any other state-of-the-art domain
prediction method. Independently folded domains of the same protein
chain are often joined by a flexible segment of amino acids, with
each half of the flexible segment counting to its adjacent
independently folded protein domain. Independently folded domains
of the same protein may be connected in a precursor molecule by a
protease cleavage site and after proteolytical processing may lie
on two different connected protein chains in the mature molecule.
Independently folded protein domains may comprise functionally
and/or structurally defined subdomains which do not take their
correct conformation without requiring support by other portions of
the protein because they are formed by discontinuous stretches of
extracellular amino acids within the primary protein sequence or
kept in their correct conformation by adjacent or other portions of
the protein.
[0046] Ther term "method for the selection", respectively the term
"selecting" denotes in the context of the present invention the
identification and isolation of one or more bispecific single chain
antibodies from a population of candidate antibodies. In
particular, the candidate antibodies are tested in separate
settings for the binding and the mediation of cytotoxicity for each
of the three different host cell populations. Populations of
bispecific single chain antibodies to be tested and methods for the
generation of such populations are described in the appended
examples. Since the method of the invention allows for the
isolation of one ore more bispecific single chain antibodies the
method is also understood as a method for the production of
bispecific single chain antibodies of the invention. Of course,
such method for the production involves the production of the
population of bispecific single chain antibodies, from which the
one or more, which bind to the membrane proximal epitopes, are
isolated.
[0047] As used herein, a "bispecific single chain antibody" denotes
a single polypeptide chain comprising two binding domains. Each
binding domain comprises one variable region from an antibody heavy
chain ("VH region"), wherein the VH region of the first binding
domain specifically binds to the CD3 molecule, and the VH region of
the second binding domain specifically binds to the extracellular
domain of a membrane protein on a target cell, e.g. to PSMA,
FAP.alpha., c-MET, endosialin/TEM1 or IGF-1R. The two binding
domains are optionally linked to one another by a short polypeptide
spacer. A non-limiting example for a polypeptide spacer is
Gly-Gly-Gly-Gly-Ser (G-G-G-G-S) and repeats thereof. Each binding
domain may additionally comprise one variable region from an
antibody light chain ("VL region"), the VH region and VL region
within each of the first and second binding domains being linked to
one another via a polypeptide linker, for example of the type
disclosed and claimed in EP 623679 B1, but in any case long enough
to allow the VH region and VL region of the first binding domain
and the VH region and VL region of the second binding domain to
pair with one another such that, together, they are able to
specifically bind to the respective first and second binding
domains.
[0048] The term "protein" is well known in the art and describes
biological compounds. Proteins comprise one or more amino acid
chains (polypeptides), whereby the amino acids are bound among one
another via a peptide bond. The term "polypeptide" as used herein
describes a group of molecules, which consists of more than 30
amino acids. In accordance with the invention, the group of
polypeptides comprises "proteins" as long as the proteins consist
of a single polypeptide chain. Also in line with the definition the
term "polypeptide" describes fragments of proteins as long as these
fragments consist of more than 30 amino acids. Polypeptides may
further form multimers such as dimers, trimers and higher
oligomers, i.e. consisting of more than one polypeptide molecule.
Polypeptide molecules forming such dimers, trimers etc. may be
identical or non-identical. The corresponding higher order
structures of such multimers are, consequently, termed homo- or
heterodimers, homo- or heterotrimers etc. An example for a
hereteromultimer is an antibody molecule, which, in its naturally
occurring form, consists of two identical light polypeptide chains
and two identical heavy polypeptide chains. The terms "polypeptide"
and "protein" also refer to naturally modified
polypeptides/proteins wherein the modification is effected e.g. by
post-translational modifications like glycosylation, acetylation,
phosphorylation and the like. Such modifications are well known in
the art.
[0049] The term "binding domain" characterizes in connection with
the present invention a domain of a polypeptide which specifically
binds to/interacts with a given target structure/antigen/epitope.
Thus, the binding domain is an "antigen-interaction-site". The term
"antigen-interaction-site" defines, in accordance with the present
invention, a motif of a polypeptide, which is able to specifically
interact with a specific antigen or a specific group of antigens,
e.g. the identical antigen in different species. Said
binding/interaction is also understood to define a "specific
recognition". The term "specifically recognizing" means in
accordance with this invention that the antibody molecule is
capable of specifically interacting with and/or binding to at least
two, preferably at least three, more preferably at least four amino
acids of an antigen, e.g. the human CD3 antigen and the target
antigens as defined herein. Such binding may be exemplified by the
specificity of a "lock-and-key-principle". Thus, specific motifs in
the amino acid sequence of the binding domain and the antigen bind
to each other as a result of their primary, secondary or tertiary
structure as well as the result of secondary modifications of said
structure. The specific interaction of the antigen-interaction-site
with its specific antigen may result as well in a simple binding of
said site to the antigen. Moreover, the specific interaction of the
binding domain/antigen-interaction-site with its specific antigen
may alternatively result in the initiation of a signal, e.g. due to
the induction of a change of the conformation of the antigen, an
oligomerization of the antigen, etc.
[0050] The term "antibody" comprises derivatives or functional
fragments thereof which still retain the binding specificity.
Techniques for the production of antibodies are well known in the
art and described, e.g. in Harlow and Lane "Antibodies, A
Laboratory Manual", Cold Spring Harbor Laboratory Press, 1988 and
Harlow and Lane "Using Antibodies: A Laboratory Manual" Cold Spring
Harbor Laboratory Press, 1999. The term "antibody" also comprises
immunoglobulins (Ig's) of different classes (i.e. IgA, IgG, IgM,
IgD and IgE) and subclasses (such as IgG1, IgG2 etc.).
[0051] The definition of the term "antibody" also includes
embodiments such as chimeric, single chain and humanized
antibodies, as well as antibody fragments, like, inter alia, Fab
fragments. Antibody fragments or derivatives further comprise
F(ab').sub.2, Fv, scFv fragments or single domain antibodies,
single variable domain antibodies or immunoglobulin single variable
domain comprising merely one variable domain, which might be VH or
VL, that specifically bind to an antigen or epitope independently
of other V regions or domains; see, for example, Harlow and Lane
(1988) and (1999), loc. cit. Such immunoglobulin single variable
domain encompasses not only an isolated antibody single variable
domain polypeptide, but also larger polypeptides that comprise one
or more monomers of an antibody single variable domain polypeptide
sequence.
[0052] Various procedures are known in the art and may be used for
the production of such antibodies and/or fragments. Thus, the
(antibody) derivatives can also be produced by peptidomimetics.
Further, techniques described for the production of single chain
antibodies (see, inter alia, U.S. Pat. No. 4,946,778) can be
adapted to produce single chain antibodies specific for elected
polypeptide(s). Also, transgenic animals may be used to express
humanized or human antibodies specific for polypeptides and fusion
proteins of this invention. For the preparation of monoclonal
antibodies, any technique, providing antibodies produced by
continuous cell line cultures can be used. Examples for such
techniques include the hybridoma technique (Kohler and Milstein
Nature 256 (1975), 495-497), the trioma technique, the human B-cell
hybridoma technique (Kozbor, Immunology Today 4 (1983), 72) and the
EBV-hybridoma technique to produce human monoclonal antibodies
(Cole et al., Monoclonal Antibodies and Cancer Therapy, Alan R.
Liss, Inc. (1985), 77-96). Surface plasmon resonance as employed in
the BIAcore system can be used to increase the efficiency of phage
antibodies which bind to an epitope of a target polypeptide, such
as CD3 (epsilon), PSMA or FAP.alpha., c-MET, TEM1 or IGF-1R
(Schier, Human Antibodies Hybridomas 7 (1996), 97-105; Malmborg, J.
Immunol. Methods 183 (1995), 7-13). It is also envisaged in the
context of this invention that the term "antibody" comprises
antibody constructs, which may be expressed in a host as described
herein below, e.g. antibody constructs which may be transfected
and/or transduced via, inter alia, viruses or plasmid vectors.
[0053] The term "specific interaction" as used in accordance with
the present invention means that the binding domain does not or
does not significantly cross-react with polypeptides which have
similar structure as those bound by the binding domain, and which
might be expressed by the same cells as the polypeptide of
interest. Cross-reactivity of a panel of binding domains under
investigation may be tested, for example, by assessing binding of
said panel of binding domains under conventional conditions (see,
e.g., Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring
Harbor Laboratory Press, 1988 and Using Antibodies: A Laboratory
Manual, Cold Spring Harbor Laboratory Press, 1999). Examples for
the specific interaction of a binding domain with a specific
antigen comprise the specificity of a ligand for its receptor. Said
definition particularly comprises the interaction of ligands, which
induce a signal upon binding to its specific receptor. Examples for
said interaction, which is also particularly comprised by said
definition, is the interaction of an antigenic determinant
(epitope) with the binding domain (antigenic binding site) of an
antibody.
[0054] According to a preferred embodiment of the method of the
invention the first binding domain binds to CD3 epsilon
(CD3.epsilon.) of human and non-chimpanzee primate. In this context
it is particularly preferred that the first binding domain capable
of binding to an epitope of human and non-chimpanzee primate
CD3.epsilon. chain binds to an epitope, which is part of an amino
acid sequence comprised in the group consisting of SEQ ID NOs. 2,
4, 6, and 8.
[0055] As used herein, "human" and "man" refers to the species Homo
sapiens. As far as the medical uses of the constructs described
herein are concerned, human patients are to be treated with the
same molecule.
[0056] The term "human" antibody as used herein is to be understood
as meaning that the bispecific single chain antibody as defined
herein, comprises (an) amino acid sequence(s) contained in the
human germline antibody repertoire. For the purposes of definition
herein, said bispecific single chain antibody may therefore be
considered human if it consists of such (a) human germline amino
acid sequence(s), i.e. if the amino acid sequence(s) of the
bispecific single chain antibody in question is (are) identical to
(an) expressed human germline amino acid sequence(s). A bispecific
single chain antibody as defined herein may also be regarded as
human if it consists of (a) sequence(s) that deviate(s) from its
(their) closest human germline sequence(s) by no more than would be
expected due to the imprint of somatic hypermutation. Additionally,
the antibodies of many non-human mammals, for example rodents such
as mice and rats, comprise VH CDR3 amino acid sequences which one
may expect to exist in the expressed human antibody repertoire as
well. Any such sequence(s) of human or non-human origin which may
be expected to exist in the expressed human repertoire would also
be considered "human" for the purposes of the present
invention.
[0057] Though T cell-engaging bispecific single chain antibodies
described in the art have great therapeutic potential for the
treatment of malignant diseases, most of these bispecific molecules
are limited in that they are species specific and recognize only
human antigen, and--due to genetic similarity--likely the
chimpanzee counterpart. The advantage of the preferred embodiment
of the invention is the provision of a bispecific single chain
antibody comprising a binding domain exhibiting cross-species
specificity to human and non-chimpanzee primate of the CD3 epsilon
chain.
[0058] Herein described examples for preferred first binding
domains bind to an N-terminal 1-27 amino acid residue polypeptide
fragment of the extracellular domain of CD3 epsilon. This 1-27
amino acid residue polypeptide fragment was surprisingly identified
which--in contrast to all other known epitopes of CD3 epsilon
described in the art--maintains its three-dimensional structural
integrity when taken out of its native environment in the CD3
complex (and optionally fused to a heterologous amino acid sequence
such as EpCAM or an immunoglobulin Fc part).
[0059] The present invention, therefore, provides for a bispecific
single chain antibody molecule comprising a first binding domain
capable of binding to an epitope of an N-terminal 1-27 amino acid
residue polypeptide fragment of the extracellular domain of CD3
epsilon (which CD3 epsilon is, for example, taken out of its native
environment and/or comprised by (presented on the surface of) a
T-cell) of human and at least one non-chimpanzee primate CD3
epsilon chain, wherein the epitope is part of an amino acid
sequence comprised in the group consisting of SEQ ID NOs. 2, 4, 6,
and 8; and a second binding domain capable of binding to
prostate-specific membrane antigen (PSMA). Preferred non-chimpanzee
primates are mentioned herein elsewhere. At least one (or a
selection thereof or all) primate(s) selected from Callithrix
jacchus; Saguinus oedipus, Saimiri sciureus, and Macaca
fascicularis (either SEQ ID 863 or 864 or both), is (are)
particularily preferred. Macaca mulatta, also known as Rhesus
Monkey is also envisaged as another preferred primate. It is thus
envisaged that antibodies of the invention bind to (are capable of
binding to) the context independent epitope of an N-terminal 1-27
amino acid residue polypeptide fragment of the extracellular domain
of CD3 epsilon of human and Callithrix jacchus, Saguinus oedipus,
Saimiri sciureus, and Macaca fascicularis (either SEQ ID 863 or 864
or both), and optionally also to Macaca mulatta. A bispecific
single chain antibody molecule comprising a first binding domain as
defined herein can be obtained (is obtainable by) or can be
manufactured in accordance with the protocol set out in the
appended Examples (in particular Example 2). To this end, it is
envisaged to (a) immunize mice with an N-terminal 1-27 amino acid
residue polypeptide fragment of the extracellular domain of CD3
epsilon of human and/or Saimiri sciureus; (b) generation of an
immune murine antibody scFv library; (c) identification of CD3
epsilon specific binders by testing the capability to bind to at
least SEQ ID NOs. 2, 4, 6, and 8.
[0060] The context-independence of the CD3 epitope provided herein
corresponds to the first 27 N-terminal amino acids of CD3 epsilon
or functional fragments of this 27 amino acid stretch. The phrase
"context-independent," as used herein in relation to the CD3
epitope means that binding of the herein described inventive
binding molecules/antibody molecules does not lead to a change or
modification of the conformation, sequence, or structure
surrounding the antigenic determinant or epitope. In contrast, the
CD3 epitope recognized by a conventional CD3 binding molecule (e.g.
as disclosed in WO 99/54440 or WO 04/106380) is localized on the
CD3 epsilon chain C-terminally to the N-terminal 1-27 amino acids
of the context-independent epitope, where it only takes the correct
conformation if it is embedded within the rest of the epsilon chain
and held in the right sterical position by heterodimerization of
the epsilon chain with either the CD3 gamma or delta chain.
Anti-CD3 binding domains as part of bispecific single chain
molecules as provided herein and generated (and directed) against a
context-independent CD3 epitope provide for a surprising clinical
improvement with regard to T cell redistribution and, thus, a more
favourable safety profile. Without being bound by theory, since the
CD3 epitope is context-independent, forming an autonomous
selfsufficient subdomain without much influence on the rest of the
CD3 complex, the CD3 binding domain of the bispecific single chain
molecules provided herein induces less allosteric changes in CD3
conformation than the conventional CD3 binding molecules (like
molecules provided in WO 99/54440 or WO 04/106380), which recognize
context-dependent CD3 epitopes.
[0061] The context-independence of the CD3 epitope which is
recognized by the CD3 binding domain of the bispecific single chain
antibodies of the invention, respectively isolated by the method of
the invention, is associated with less or no T cell redistribution
(T cell redistribution equates with an initial episode of drop and
subsequent recovery of absolute T cell counts) during the starting
phase of treatment with said bispecific single chain antibody. This
results in a better safety profile of the bispecific single chain
antibodies of the invention compared to conventional CD3 binding
molecules known in the art, which recognize context-dependent CD3
epitopes. Particularly, because T cell redistribution during the
starting phase of treatment with CD3 binding molecules is a major
risk factor for adverse events, like CNS adverse events, the
bispecific single chain antibodies of the invention by recognizing
a context-independent rather than a context-dependent CD3 epitope
has a substantial safety advantage over the CD3 binding molecules
known in the art. Patients with such CNS adverse events related to
T cell redistribution during the starting phase of treatment with
conventional CD3 binding molecules usually suffer from confusion
and disorientation, in some cases also from urinary incontinence.
Confusion is a change in mental status in which the patient is not
able to think with his or her usual level of clarity. The patient
usually has difficulties to concentrate and thinking is not only
blurred and unclear but often significantly slowed down. Patients
with CNS adverse events related to T cell redistribution during the
starting phase of treatment with conventional CD3 binding molecules
may also suffer from loss of memory. Frequently, the confusion
leads to the loss of ability to recognize people, places, time or
the date. Feelings of disorientation are common in confusion, and
the decision-making ability is impaired. CNS adverse events related
to T cell redistribution during the starting phase of treatment
with conventional CD3 binding molecules may further comprise
blurred speech and/or word finding difficulties. This disorder may
impair both, the expression and understanding of language as well
as reading and writing. Besides urinary incontinence, vertigo and
dizziness may also accompany CNS adverse events related to T cell
redistribution during the starting phase of treatment with
conventional CD3 binding molecules in some patients.
[0062] The maintenance of the three-dimensional structure within
the mentioned 27 amino acid N-terminal polypeptide fragment of CD3
epsilon can be used for the generation of, preferably human,
binding domains which are capable of binding to the N-terminal CD3
epsilon polypeptide fragment in vitro and to the native (CD3
epsilon subunit of the) CD3 complex on T cells in vivo with the
same binding affinity. These data strongly indicate that the
N-terminal fragment as described herein forms a tertiary
conformation, which is similar to its structure normally existing
in vivo. A very sensitive test for the importance of the structural
integrity of the amino acids 1-27 of the N-terminal polypeptide
fragment of CD3 epsilon was performed. Individual amino acids of
amino acids 1-27 of the N-terminal polypeptide fragment of CD3
epsilon were changed to alanine (alanine scanning) to test the
sensitivity of the amino acids 1-27 of the N-terminal polypeptide
fragment of CD3 epsilon for minor disruptions.
[0063] Unexpectedly, it has been found that the thus isolated,
preferably human, bispecific single chain antibody of the invention
not only recognizes the human N-terminal fragment of CD3 epsilon,
but also the corresponding homologous fragments of CD3 epsilon of
various primates, including New-World Monkeys (Marmoset, Callithrix
jacchus; Saguinus oedipus; Saimiri sciureus) and Old-World Monkeys
(Macaca fascicularis, also known as Cynomolgus Monkey; or Macaca
mulatta, also known as Rhesus Monkey). Thus, multi-primate
specificity of the bispecific single chain antibodies of the
invention can be detected. The multi-primate specificity of the
biding domains of the invention is defined herein as cross-species
specificity.
[0064] The amino acid sequence of the aformentioned N-terminal
fragments of CD3 epsilon are depicted in SEQ ID No. 2 (human), SEQ
ID No. 4 (Callithrix jacchus); SEQ ID No. 6 (Saguinus oedipus); SEQ
ID No. 8 (Saimiri sciureus); SEQ ID No. 863
QDGNEEMGSITQTPYQVSISGTTILTC or SEQ ID No. 864
QDGNEEMGSITQTPYQVSISGTTVILT (Macaca fascicularis, also known as
Cynomolgus Monkey), and SEQ ID No. 865 QDGNEEMGSITQTPYHVSISGTTVILT
(Macaca mulatta, also known as Rhesus Monkey).
[0065] The term "cross-species specificity" or "interspecies
specificity" as used herein means binding of a binding domain
described herein to the same target molecule in humans and
non-chimpanzee primates. Thus, "cross-species specificity" or
"interspecies specificity" is to be understood as an interspecies
reactivity to the same molecule "X" expressed in different species,
but not to a molecule other than "X". Cross-species specificity of
a monoclonal antibody recognizing e.g. human CD3 epsilon, to a
non-chimpanzee primate CD3 epsilon, e.g. macaque CD3 epsilon, can
be determined, for instance, by FACS analysis. The FACS analysis is
carried out in a way that the respective monoclonal antibody is
tested for binding to human and non-chimpanzee primate cells, e.g.
macaque cells, expressing said human and non-chimpanzee primate CD3
epsilon antigens, respectively. An appropriate assay is shown in
the following examples. The above-mentioned subject matter applies
mutatis mutandis for the targe antigens PSMA, FAP.alpha.,
endosialin (TEM1), c-MET and IGF-1R: Cross-species specificity of a
monoclonal antibody recognizing e.g. human PSMA, to a
non-chimpanzee primate PSMA, e.g. macaque PSMA, can be determined,
for instance, by FACS analysis. The FACS analysis is carried out in
a way that the respective monoclonal antibody is tested for binding
to human and non-chimpanzee primate cells, e.g. macaque cells,
expressing said human and non-chimpanzee primate PSMA antigens,
respectively.
[0066] As used herein, CD3 epsilon denotes a molecule expressed as
part of the T cell receptor and has the meaning as typically
ascribed to it in the prior art. In human, it encompasses in
individual or independently combined form all known CD3 subunits,
for example CD3 epsilon, CD3 delta, CD3 gamma, CD3 zeta, CD3 alpha
and CD3 beta. The non-chimpanzee primate, non-human CD3 antigens as
referred to herein are, for example, Macaca fascicularis CD3 and
Macaca mulatta CD3. In Macaca fascicularis, it encompasses CD3
epsilon FN-18 negative and CD3 epsilon FN-18 positive, CD3 gamma
and CD3 delta. In Macaca mulatta, it encompasses CD3 epsilon, CD3
gamma and CD3 delta. Preferably, said CD3 as used herein is CD3
epsilon.
[0067] The human CD3 epsilon is indicated in GenBank Accession No.
NM_000733 and comprises SEQ ID NO. 1. The human CD3 gamma is
indicated in GenBank Accession NO. NM_000073. The human CD3 delta
is indicated in GenBank Accession No. NM_000732.
[0068] The CD3 epsilon "FN-18 negative" of Macaca fascicularis
(i.e. CD3 epsilon not recognized by monoclonal antibody FN-18 due
to a polymorphism as set forth above) is indicated in GenBank
Accession No. AB073994.
[0069] The CD3 epsilon "FN-18 positive" of Macaca fascicularis
(i.e. CD3 epsilon recognized by monoclonal antibody FN-18) is
indicated in GenBank Accession No. AB073993. The CD3 gamma of
Macaca fascicularis is indicated in GenBank Accession No. AB073992.
The CD3 delta of Macaca fascicularis is indicated in GenBank
Accession No. AB073991.
[0070] The nucleic acid sequences and amino acid sequences of the
respective CD3 epsilon, gamma and delta homologs of Macaca mulatta
can be identified and isolated by recombinant techniques described
in the art (Sambrook et al. Molecular Cloning: A Laboratory Manual;
Cold Spring Harbor Laboratory Press, 3.sup.rd edition 2001). This
applies mutatis mutandis to the CD3 epsilon, gamma and delta
homologs of other non-chimpanzee primates as defined herein. The
identification of the amino acid sequence of Callithrix jacchus,
Saimiri sciureus and Saguinus oedipus is described in the appended
examples. The amino acid sequence of the extracellular domain of
the CD3 epsilon of Callithrix jacchus is depicted in SEQ ID NO: 3,
the one of Saguinus oedipus is depicted in SEQ ID NO: 5 and the one
of Saimiri sciureus is depicted in SEQ ID NO: 7.
[0071] In line with the above, the term "epitope" defines an
antigenic determinant, which is specifically bound/identified by a
binding domain as defined herein. The binding domain may
specifically bind to/interact with conformational or continuous
epitopes, which are unique for the target structure, e.g. the human
and non-chimpanzee primate CD3 epsilon chain. A conformational or
discontinuous epitope is characterized for polypeptide antigens by
the presence of two or more discrete amino acid residues which are
separated in the primary sequence, but come together on the surface
of the molecule when the polypeptide folds into the native
protein/antigen (Sela, (1969) Science 166, 1365 and Laver, (1990)
Cell 61, 553-6). The two or more discrete amino acid residues
contributing to the epitope are present on separate sections of one
or more polypeptide chain(s). These residues come together on the
surface of the molecule when the polypeptide chain(s) fold(s) into
a three-dimensional structure to constitute the epitope. In
contrast, a continuous or linear epitope consists of two or more
discrete amino acid residues, which are present in a single linear
segment of a polypeptide chain. Within the present invention, a
"context-dependent" CD3 epitope refers to the conformation of said
epitope. Such a context-dependent epitope, localized on the epsilon
chain of CD3, can only develop its correct conformation if it is
embedded within the rest of the epsilon chain and held in the right
position by heterodimerization of the epsilon chain with either CD3
gamma or delta chain. In contrast, a context-independent CD3
epitope as provided herein refers to an N-terminal 1-27 amino acid
residue polypeptide or a functional fragment thereof of CD3
epsilon. This N-terminal 1-27 amino acid residue polypeptide or a
functional fragment thereof maintains its three-dimensional
structural integrity and correct conformation when taken out of its
native environment in the CD3 complex. The context-independency of
the N-terminal 1-27 amino acid residue polypeptide or a functional
fragment thereof, which is part of the extracellular domain of CD3
epsilon, represents, thus, an epitope which is completely different
to the epitopes of CD3 epsilon described in connection with a
method for the preparation of human binding molecules in WO
2004/106380. Said method used solely expressed recombinant CD3
epsilon. The conformation of this solely expressed recombinant CD3
epsilon differed from that adopted in its natural form, that is,
the form in which the CD3 epsilon subunit of the TCR/CD3 complex
exists as part of a noncovalent complex with either the CD3 delta
or the CD3-gamma subunit of the TCR/CD3 complex. When such solely
expressed recombinant CD3 epsilon protein is used as an antigen for
selection of antibodies from an antibody library, antibodies
specific for this antigen are identified from the library although
such a library does not contain antibodies with specificity for
self-antigens/autoantigens. This is due to the fact that solely
expressed recombinant CD3 epsilon protein does not exist in vivo;
it is not an autoantigen. Consequently, subpopulations of B cells
expressing antibodies specific for this protein have not been
depleted in vivo; an antibody library constructed from such B cells
would contain genetic material for antibodies specific for solely
expressed recombinant CD3 epsilon protein.
[0072] However, since the context-independent N-terminal 1-27 amino
acid residue polypeptide or a functional fragment thereof is an
epitope, which folds in its native form, binding domains in line
with the present invention cannot be identified by methods based on
the approach described in WO 2004/106380. Therefore, it could be
verified in tests that binding molecules as disclosed in WO
2004/106380 are not capable of binding to the N-terminal 1-27 amino
acid residues of the CD3 epsilon chain. Hence, conventional
anti-CD3 binding molecules or anti-CD3 antibody molecules (e.g. as
disclosed in WO 99/54440) bind CD3 epsilon chain at a position
which is more C-terminally located than the context-independent
N-terminal 1-27 amino acid residue polypeptide or a functional
fragment provided herein. Prior art antibody molecules OKT3 and
UCHT-1 have also a specificity for the epsilon-subunit of the
TCR/CD3 complex between amino acid residues 35 to 85 and,
accordingly, the epitope of these antibodies is also more
C-terminally located. In addition, UCHT-1 binds to the CD3 epsilon
chain in a region between amino acid residues 43 to 77
(Tunnacliffe, Int. Immunol. 1 (1989), 546-50; Kjer-Nielsen, PNAS
101, (2004), 7675-7680; Salmeron, J. Immunol. 147 (1991), 3047-52).
Therefore, prior art anti-CD3 molecules do not bind to and are not
directed against the herein defined context-independent N-terminal
1-27 amino acid residue epitope (or a functional fragment thereof).
In particular, the state of the art fails to provide anti-CD3
molecules which specifically binds to the context-independent
N-terminal 1-27 amino acid residue epitope and which are
cross-species specific, i.e. bind to human and non-chimpanzee
primate CD3 epsilon.
[0073] As used herein, the term "humanized", "humanization",
"human-like" or grammatically related variants thereof are used
interchangeably to refer to a bispecific single chain antibody
comprising in at least one of its binding domains at least one
complementarity determining region ("CDR") from a non-human
antibody or fragment thereof. Humanization approaches are described
for example in WO 91/09968 and U.S. Pat. No. 6,407,213. As
non-limiting examples, the term encompasses the case in which a
variable region of at least one binding domain comprises a single
CDR region, for example the third CDR region of the VH (CDRH3),
from another non-human animal, for example a rodent, as well as the
case in which a or both variable region/s comprise at each of their
respective first, second and third CDRs the CDRs from said
non-human animal. In the event that all CDRs of a binding domain of
the bispecific single chain antibody have been replaced by their
corresponding equivalents from, for example, a rodent, one
typically speaks of "CDR-grafting", and this term is to be
understood as being encompassed by the term "humanized" or
grammatically related variants thereof as used herein. The term
"humanized" or grammatically related variants thereof also
encompasses cases in which, in addition to replacement of one or
more CDR regions within a VH and/or VL of the first and/or second
binding domain further mutation/s (e.g. substitutions) of at least
one single amino acid residue/s within the framework ("FR") regions
between the CDRs has/have been effected such that the amino acids
at that/those positions correspond/s to the amino acid/s at
that/those position/s in the animal from which the CDR regions used
for replacement is/are derived. As is known in the art, such
individual mutations are often made in the framework regions
following CDR-grafting in order to restore the original binding
affinity of the non-human antibody used as a CDR-donor for its
target molecule. The term "humanized" may further encompass (an)
amino acid substitution(s) in the CDR regions from a non-human
animal to the amino acid(s) of a corresponding CDR region from a
human antibody, in addition to the amino acid substitutions in the
framework regions as described above.
[0074] As used herein, the term "homolog" or "homology" is to be
understood as follows: Homology among proteins and DNA is often
concluded on the basis of sequence similarity, especially in
bioinformatics. For example, in general, if two or more genes have
highly similar DNA sequences, it is likely that they are
homologous. But sequence similarity may arise from different
ancestors: short sequences may be similar by chance, and sequences
may be similar because both were selected to bind to a particular
protein, such as a transcription factor. Such sequences are similar
but not homologous. Sequence regions that are homologous are also
called conserved. This is not to be confused with conservation in
amino acid sequences in which the amino acid at a specific position
has changed but the physio-chemical properties of the amino acid
remain unchanged. Homologous sequences are of two types:
orthologous and paralogous. Homologous sequences are orthologous if
they were separated by a speciation event: when a species diverges
into two separate species, the divergent copies of a single gene in
the resulting species are said to be orthologous. Orthologs, or
orthologous genes, are genes in different species that are similar
to each other because they originated from a common ancestor. The
strongest evidence that two similar genes are orthologous is the
result of a phylogenetic analysis of the gene lineage. Genes that
are found within one clade are orthologs, descended from a common
ancestor. Orthologs often, but not always, have the same function.
Orthologous sequences provide useful information in taxonomic
classification studies of organisms. The pattern of genetic
divergence can be used to trace the relatedness of organisms. Two
organisms that are very closely related are likely to display very
similar DNA sequences between two orthologs. Conversely, an
organism that is further removed evolutionarily from another
organism is likely to display a greater divergence in the sequence
of the orthologs being studied. Homologous sequences are paralogous
if they were separated by a gene duplication event: if a gene in an
organism is duplicated to occupy two different positions in the
same genome, then the two copies are paralogous. A set of sequences
that are paralogous are called paralogs of each other. Paralogs
typically have the same or similar function, but sometimes do not:
due to lack of the original selective pressure upon one copy of the
duplicated gene, this copy is free to mutate and acquire new
functions. An example can be found in rodents such as rats and
mice. Rodents have a pair of paralogous insulin genes, although it
is unclear if any divergence in function has occurred. Paralogous
genes often belong to the same species, but this is not necessary:
for example, the hemoglobin gene of humans and the myoglobin gene
of chimpanzees are paralogs. This is a common problem in
bioinformatics: when genomes of different species have been
sequenced and homologous genes have been found, one can not
immediately conclude that these genes have the same or similar
function, as they could be paralogs whose function has
diverged.
[0075] As used herein, a "non-chimpanzee primate" or "non-chimp
primate" or grammatical variants thereof refers to any primate
animal (i.e. not human) other than chimpanzee, i.e. other than an
animal of belonging to the genus Pan, and including the species Pan
paniscus and Pan troglodytes, also known as Anthropopithecus
troglodytes or Simia satyrus. It will be understood, however, that
it is possible that the antibodies of the invention can also bind
with their first and/or second binding domain to the respective
epitopes/fragments etc. of said chimpanzees. The intention is
merely to avoid animal tests which are carried out with
chimpanzees, if desired. It is thus also envisaged that in another
embodiment the antibodies of the present invention also bind with
their first and/or second binding domain to the respective epitopes
of chimpanzees. A "primate", "primate species", "primates" or
grammatical variants thereof denote/s an order of eutherian mammals
divided into the two suborders of prosimians and anthropoids and
comprising apes, monkeys and lemurs. Specifically, "primates" as
used herein comprises the suborder Strepsirrhini (non-tarsier
prosimians), including the infraorder Lemuriformes (itself
including the superfamilies Cheirogaleoidea and Lemuroidea), the
infraorder Chiromyiformes (itself including the family
Daubentoniidae) and the infraorder Lorisiformes (itself including
the families Lorisidae and Galagidae). "Primates" as used herein
also comprises the suborder Haplorrhini, including the infraorder
Tarsiiformes (itself including the family Tarsiidae), the
infraorder Simiiformes (itself including the Platyrrhini, or
New-World monkeys, and the Catarrhini, including the
Cercopithecidea, or Old-World Monkeys).
[0076] The non-chimpanzee primate species may be understood within
the meaning of the invention to be a lemur, a tarsier, a gibbon, a
marmoset (belonging to New-World Monkeys of the family Cebidae) or
an Old-World Monkey (belonging to the superfamily
Cercopithecoidea).
[0077] As used herein, an "Old-World Monkey" comprises any monkey
falling in the superfamily Cercopithecoidea, itself subdivided into
the families: the Cercopithecinae, which are mainly African but
include the diverse genus of macaques which are Asian and North
African; and the Colobinae, which include most of the Asian genera
but also the African colobus monkeys.
[0078] Specifically, within the subfamily Cercopithecinae, an
advantageous non-chimpanzee primate may be from the Tribe
Cercopithecini, within the genus Allenopithecus (Allen's Swamp
Monkey, Allenopithecus nigroviridis); within the genus Miopithecus
(Angolan Talapoin, Miopithecus talapoin; Gabon Talapoin,
Miopithecus ogouensis); within the genus Erythrocebus (Patas
Monkey, Erythrocebus patas); within the genus Chlorocebus (Green
Monkey, Chlorocebus sabaceus; Grivet, Chlorocebus aethiops; Bale
Mountains Vervet, Chlorocebus djamdjamensis; Tantalus Monkey,
Chlorocebus tantalus; Vervet Monkey, Chlorocebus pygerythrus;
Malbrouck, Chlorocebus cynosuros); or within the genus
Cercopithecus (Dryas Monkey or Salongo Monkey, Cercopithecus dryas;
Diana Monkey, Cercopithecus diana; Roloway Monkey, Cercopithecus
roloway; Greater Spot-nosed Monkey, Cercopithecus nictitans; Blue
Monkey, Cercopithecus mitis; Silver Monkey, Cercopithecus doggetti;
Golden Monkey, Cercopithecus kandti; Sykes's Monkey, Cercopithecus
albogularis; Mona Monkey, Cercopithecus mona; Campbell's Mona
Monkey, Cercopithecus campbelli; Lowe's Mona Monkey, Cercopithecus
lowei; Crested Mona Monkey, Cercopithecus pogonias; Wolf's Mona
Monkey, Cercopithecus wolfi; Dent's Mona Monkey, Cercopithecus
denti; Lesser Spot-nosed Monkey, Cercopithecus petaurista;
White-throated Guenon, Cercopithecus erythrogaster; Sclater's
Guenon, Cercopithecus sclateri; Red-eared Guenon, Cercopithecus
erythrotis; Moustached Guenon, Cercopithecus cephus; Red-tailed
Monkey, Cercopithecus ascanius; L'Hoest's Monkey, Cercopithecus
lhoesti; Preuss's Monkey, Cercopithecus preussi; Sun-tailed Monkey,
Cercopithecus solatus; Hamlyn's Monkey or Owl-faced Monkey,
Cercopithecus hamlyni; De Brazza's Monkey, Cercopithecus
neglectus).
[0079] Alternatively, an advantageous non-chimpanzee primate, also
within the subfamily Cercopithecinae but within the Tribe
Papionini, may be from within the genus Macaca (Barbary Macaque,
Macaca sylvanus; Lion-tailed Macaque, Macaca silenus; Southern
Pig-tailed Macaque or Beruk, Macaca nemestrina; Northern Pig-tailed
Macaque, Macaca leonina; Pagai Island Macaque or Bokkoi, Macaca
pagensis; Siberut Macaque, Macaca siberu; Moor Macaque, Macaca
maura; Booted Macaque, Macaca ochreata; Tonkean Macaque, Macaca
tonkeana; Heck's Macaque, Macaca hecki; Gorontalo Macaque, Macaca
nigriscens; Celebes Crested Macaque or Black "Ape", Macaca nigra;
Cynomolgus monkey or Crab-eating Macaque or Long-tailed Macaque or
Kera, Macaca fascicularis; Stump-tailed Macaque or Bear Macaque,
Macaca arctoides; Rhesus Macaque, Macaca mulatta; Formosan Rock
Macaque, Macaca cyclopis; Japanese Macaque, Macaca fuscata; Toque
Macaque, Macaca sinica; Bonnet Macaque, Macaca radiata; Barbary
Macaque, Macaca sylvanmus; Assam Macaque, Macaca assamensis;
Tibetan Macaque or Milne-Edwards' Macaque, Macaca thibetana;
Arunachal Macaque or Munzala, Macaca munzala); within the genus
Lophocebus (Gray-cheeked Mangabey, Lophocebus albigena; Lophocebus
albigena albigena; Lophocebus albigena osmani; Lophocebus albigena
johnstoni; Black Crested Mangabey, Lophocebus aterrimus;
Opdenbosch's Mangabey, Lophocebus opdenboschi; Highland Mangabey,
Lophocebus kipunji); within the genus Papio (Hamadryas Baboon,
Papio hamadryas; Guinea Baboon, Papio papio; Olive Baboon, Papio
anubis; Yellow Baboon, Papio cynocephalus; Chacma Baboon, Papio
ursinus); within the genus Theropithecus (Gelada, Theropithecus
gelada); within the genus Cercocebus (Sooty Mangabey, Cercocebus
atys; Cercocebus atys atys; Cercocebus atys lunulatus; Collared
Mangabey, Cercocebus torquatus; Agile Mangabey, Cercocebus agilis;
Golden-bellied Mangabey, Cercocebus chrysogaster; Tana River
Mangabey, Cercocebus galeritus; Sanje Mangabey, Cercocebus sanjei);
or within the genus Mandrillus (Mandrill, Mandrillus sphinx; Drill,
Mandrillus leucophaeus).
[0080] Most preferred is Macaca fascicularis (also known as
Cynomolgus monkey and, therefore, in the Examples named
"Cynomolgus") and Macaca mulatta (rhesus monkey, named
"rhesus").
[0081] Within the subfamily Colobinae, an advantageous
non-chimpanzee primate may be from the African group, within the
genus Colobus (Black Colobus, Colobus satanas; Angola Colobus,
Colobus angolensis; King Colobus, Colobus polykomos; Ursine
Colobus, Colobus vellerosus; Mantled Guereza, Colobus guereza);
within the genus Piliocolobus (Western Red Colobus, Piliocolobus
badius; Piliocolobus badius badius; Piliocolobus badius temminckii;
Piliocolobus badius waldronae; Pennant's Colobus, Piliocolobus
pennantii; Piliocolobus pennantii pennantii; Piliocolobus pennantii
epieni; Piliocolobus pennantii bouvieri; Preuss's Red Colobus,
Piliocolobus preussi; Thollon's Red Colobus, Piliocolobus tholloni;
Central African Red Colobus, Piliocolobus foai; Piliocolobus foai
foai; Piliocolobus foai ellioti; Piliocolobus foai oustaleti;
Piliocolobus foai semlikiensis; Piliocolobus foai parmentierorum;
Ugandan Red Colobus, Piliocolobus tephrosceles; Uzyngwa Red
Colobus, Piliocolobus gordonorum; Zanzibar Red Colobus,
Piliocolobus kirkii; Tana River Red Colobus, Piliocolobus
rufomitratus); or within the genus Procolobus (Olive Colobus,
Procolobus verus).
[0082] Within the subfamily Colobinae, an advantageous
non-chimpanzee primate may alternatively be from the Langur (leaf
monkey) group, within the genus Semnopithecus (Nepal Gray Langur,
Semnopithecus schistaceus; Kashmir Gray Langur, Semnopithecus ajax;
Tarai Gray Langur, Semnopithecus hector; Northern Plains Gray
Langur, Semnopithecus entellus; Black-footed Gray Langur,
Semnopithecus hypoleucos; Southern Plains Gray Langur,
Semnopithecus dussumieri; Tufted Gray Langur, Semnopithecus priam);
within the T. vetulus group or the genus Trachypithecus
(Purple-faced Langur, Trachypithecus vetulus; Nilgiri Langur,
Trachypithecus johnii); within the T. cristatus group of the genus
Trachypithecus (Javan Lutung, Trachypithecus auratus; Silvery Leaf
Monkey or Silvery Lutung, Trachypithecus cristatus; Indochinese
Lutung, Trachypithecus germaini; Tenasserim Lutung, Trachypithecus
barbel); within the T. obscurus group of the genus Trachypithecus
(Dusky Leaf Monkey or Spectacled Leaf Monkey, Trachypithecus
obscurus; Phayre's Leaf Monkey, Trachypithecus phayrei); within the
T. pileatus group of the genus Trachypithecus (Capped Langur,
Trachypithecus pileatus; Shortridge's Langur, Trachypithecus
shortridgei; Gee's Golden Langur, Trachypithecus geei); within the
T. francoisi group of the genus Trachypithecus (Francois' Langur,
Trachypithecus francoisi; Hatinh Langur, Trachypithecus
hatinhensis; White-headed Langur, Trachypithecus poliocephalus;
Laotian Langur, Trachypithecus laotum; Delacour's Langur,
Trachypithecus delacouri; Indochinese Black Langur, Trachypithecus
ebenus); or within the genus Presbytis (Sumatran Surili, Presbytis
melalophos; Banded Surili, Presbytis femoralis; Sarawak Surili,
Presbytis chrysomelas; White-thighed Surili, Presbytis siamensis;
White-fronted Surili, Presbytis frontata; Javan Surili, Presbytis
comata; Thomas's Langur, Presbytis thomasi; Hose's Langur,
Presbytis hosei; Maroon Leaf Monkey, Presbytis rubicunda; Mentawai
Langur or Joja, Presbytis potenziani; Natuna Island Surili,
Presbytis natunae).
[0083] Within the subfamily Colobinae, an advantageous
non-chimpanzee primate may alternatively be from the Odd-Nosed
group, within the genus Pygathrix (Red-shanked Douc, Pygathrix
nemaeus; Black-shanked Douc, Pygathrix nigripes; Gray-shanked Douc,
Pygathrix cinerea); within the genus Rhinopithecus (Golden
Snub-nosed Monkey, Rhinopithecus roxellana; Black Snub-nosed
Monkey, Rhinopithecus bieti; Gray Snub-nosed Monkey, Rhinopithecus
brelichi; Tonkin Snub-nosed Langur, Rhinopithecus avunculus);
within the genus Nasalis (Proboscis Monkey, Nasalis larvatus); or
within the genus Simias (Pig-tailed Langur, Simias concolor).
[0084] As used herein, the term "marmoset" denotes any New-World
Monkeys of the genus Callithrix, for example belonging to the
Atlantic marmosets of subgenus Callithrix (sic!) (Common Marmoset,
Callithrix (Callithrix) jacchus; Black-tufted Marmoset, Callithrix
(Callithrix) penicillata; Wied's Marmoset, Callithrix (Callithrix)
kuhlii; White-headed Marmoset, Callithrix (Callithrix) geoffroyi;
Buffy-headed Marmoset, Callithrix (Callithrix) flaviceps;
Buffy-tufted Marmoset, Callithrix (Callithrix) aurita); belonging
to the Amazonian marmosets of subgenus Mico (Rio Acari Marmoset,
Callithrix (Mico) acariensis; Manicore Marmoset, Callithrix (Mico)
manicorensis; Silvery Marmoset, Callithrix (Mico) argentata; White
Marmoset, Callithrix (Mico) leucippe; Emilia's Marmoset, Callithrix
(Mico) emiliae; Black-headed Marmoset, Callithrix (Mico) nigriceps;
Marca's Marmoset, Callithrix (Mico)marcai; Black-tailed Marmoset,
Callithrix (Mico) melanura; Santarem Marmoset, Callithrix (Mico)
humeralifera; Maues Marmoset, Callithrix (Mico) mauesi;
Gold-and-white Marmoset, Callithrix (Mico) chrysoleuca;
Hershkovitz's Marmoset, Callithrix (Mico) intermedia; Satere
Marmoset, Callithrix (Mico) saterei); Roosmalens' Dwarf Marmoset
belonging to the subgenus Callibella (Callithrix (Callibella)
humilis); or the Pygmy Marmoset belonging to the subgenus Cebuella
(Callithrix (Cebuella) pygmaea).
[0085] Other genera of the New-World Monkeys comprise tamarins of
the genus Saguinus (comprising the S. oedipus-group, the S. midas
group, the S. nigricollis group, the S. mystax group, the S.
bicolor group and the S. inustus group) and squirrel monkeys of the
genus Saimiri (e.g. Saimiri sciureus, Saimiri oerstedii, Saimiri
ustus, Saimiri boliviensis, Saimiri vanzolini).
[0086] Advantageously, the present invention provides also target
antigenxCD3 bispecific single chain antibodies comprising a second
binding domain which binds both to the human target antigen and to
the macaque target antigen homolog, i.e. the homolog of a
non-chimpanzee primate. In a preferred embodiment, the bispecific
single chain antibody thus comprises a second binding domain
exhibiting cross-species specificity to the human and a
non-chimpanzee primate target antigen. In this case, the identical
bispecific single chain antibody molecule can be used both for
preclinical evaluation of safety, activity and/or pharmacokinetic
profile of these binding domains in primates and as drug in humans.
Put in other words, the same molecule can be used in preclinical
animal studies as well as in clinical studies in humans. This leads
to highly comparable results and a much-increased predictive power
of the animal studies compared to species-specific surrogate
molecules. Since both the CD3 and the target antigen binding domain
of the target antigenxCD3 bispecific single chain antibody of the
invention are cross-species specific, i.e. reactive with the human
and non-chimpanzee primates' antigens, it can be used both for
preclinical evaluation of safety, activity and/or pharmacokinetic
profile of these binding domains in primates and--in the identical
form--as drug in humans. It will be understood that in a preferred
embodiment, the cross-species specificity of the first and second
binding domain of the antibodies of the invention is identical.
[0087] It has been found in the present invention that it is
possible to generate a, preferably human, target antigenxCD3
bispecific single chain antibody wherein the identical molecule can
be used in preclinical animal testing, as well as clinical studies
and even in therapy in human. This is due to the unexpected
identification of the, preferably human, target antigenxCD3
bispecific single chain antibody, which, in addition to binding to
human CD3 epsilon and target antigen, respectively, (and due to
genetic similarity likely to the chimpanzee counterpart), also
binds to the homologs of said antigens of non-chimpanzee primates,
including New-World Monkeys and Old-World Monkeys. The preferably
human, target antigenxCD3 bispecific single chain antibody of the
invention can be used as therapeutic agent against various
diseases, including, but not limited, to cancer. In view of the
above, the need to construct a surrogate target antigenxCD3
bispecific single chain antibody for testing in a phylogenetic
distant (from humans) species disappears. As a result, the
identical molecule can be used in animal preclinical testing as is
intended to be administered to humans in clinical testing as well
as following market approval and therapeutic drug administration.
The ability to use the same molecule for preclinical animal testing
as in later administration to humans virtually eliminates, or at
least greatly reduces, the danger that the data obtained in
preclinical animal testing have limited applicability to the human
case. In short, obtaining preclinical safety data in animals using
the same molecule as will actually be administered to humans does
much to ensure the applicability of the data to a human-relevant
scenario. In contrast, in conventional approaches using surrogate
molecules, said surrogate molecules have to be molecularly adapted
to the animal test system used for preclinical safety assessment.
Thus, the molecule to be used in human therapy in fact differs in
sequence and also likely in structure from the surrogate molecule
used in preclinical testing in pharmacokinetic parameters and/or
biological activity, with the consequence that data obtained in
preclinical animal testing have limited
applicability/transferability to the human case. The use of
surrogate molecules requires the construction, production,
purification and characterization of a completely new construct.
This leads to additional development costs and time necessary to
obtain that molecule. In sum, surrogates have to be developed
separately in addition to the actual drug to be used in human
therapy, so that two lines of development for two molecules have to
be carried out. Therefore, a major advantage of the, preferably
human, target antigenxCD3 bispecific single chain antibody of the
invention exhibiting cross-species specificity described herein is
that the identical molecule can be used for therapeutic agents in
humans and in preclinical animal testing.
[0088] It is preferred that at least one of said first or second
binding domains of the bispecific single chain antibody of the
invention is CDR-grafted, humanized or human, as set forth in more
detail below. Preferably, both the first and second binding domains
of the bispecific single chain antibody of the invention are
CDR-grafted, humanized or human. For the preferably human, target
antigenxCD3 bispecific single chain antibody of the invention, the
generation of an immune reaction against said binding molecule is
excluded to the maximum possible extent upon administration of the
molecule to human patients.
[0089] Another major advantage of the, preferably human, target
antigenxCD3 bispecific single chain antibody of the invention is
its applicability for preclinical testing in various primates. The
behavior of a drug candidate in animals should ideally be
indicative of the expected behavior of this drug candidate upon
administration to humans. As a result, the data obtained from such
preclinical testing should therefore generally have a highly
predictive power for the human case. However, as learned from the
tragic outcome of the recent Phase I clinical trial on TGN1412 (a
CD28 monoclonal antibody), a drug candidate may act differently in
a primate species than in humans: Whereas in preclinical testing of
said antibody no or only limited adverse effects have been observed
in animal studies performed with cynomolgus monkeys, six human
patients developed multiple organ failure upon administration of
said antibody (Lancet 368 (2006), 2206-7). The results of these
dramatic, non-desired negative events suggest that it may not be
sufficient to limit preclinical testing to only one (non-chimpanzee
primate) species. The fact that the target antigenxCD3 bispecific
single chain antibody of the invention binds to a series of
New-World and Old-World Monkeys may help to overcome the problems
faced in the case mentioned above. Accordingly, the present
invention provides means and methods for minimizing species
differences in effects when drugs for human therapy are being
developed and tested.
[0090] With the, preferably human, cross-species specific target
antigenxCD3 bispecific single chain antibody of the invention it is
also no longer necessary to adapt the test animal to the drug
candidate intended for administration to humans, such as e.g. the
creation of transgenic animals. The, preferably human, target
antigenxCD3 bispecific single chain antibody of the invention
exhibiting cross-species specificity according to the uses and the
methods of invention can be directly used for preclinical testing
in non-chimpanzee primates, without any genetic manipulation of the
animals. As well known to those skilled in the art, approaches in
which the test animal is adapted to the drug candidate always bear
the risk that the results obtained in the preclinical safety
testing are less representative and predictive for humans due to
the modification of the animal. For example, in transgenic animals,
the proteins encoded by the transgenes are often highly
over-expressed. Thus, data obtained for the biological activity of
an antibody against this protein antigen may be limited in their
predictive value for humans in which the protein is expressed at
much lower, more physiological levels.
[0091] A further advantage of the uses of the preferably human
target antigenxCD3 bispecific single chain antibody of the
invention exhibiting cross-species specificity is the fact that
chimpanzees as an endangered species are avoided for animal
testing.
[0092] Chimpanzees are the closest relatives to humans and were
recently grouped into the family of hominids based on the genome
sequencing data (Wildman et al., PNAS 100 (2003), 7181). Therefore,
data obtained with chimpanzee is generally considered to be highly
predictive for humans. However, due to their status as endangered
species, the number of chimpanzees, which can be used for medical
experiments, is highly restricted. As stated above, maintenance of
chimpanzees for animal testing is therefore both costly and
ethically problematic. The uses of the, preferably human, target
antigenxCD3 bispecific single chain antibody of the invention avoid
both ethical objections and financial burden during preclinical
testing without prejudicing the quality, i.e. applicability, of the
animal testing data obtained. In light of this, the uses of the,
preferably human, target antigenxCD3 bispecific single chain
antibody of the invention provide for a reasonable alternative for
studies in chimpanzees.
[0093] A still further advantage of the, preferably human, target
antigenxCD3 bispecific single chain antibody of the invention is
the ability of extracting multiple blood samples when using it as
part of animal preclinical testing, for example in the course of
pharmacokinetic animal studies. Multiple blood extractions can be
much more readily obtained with a non-chimpanzee primate than with
lower animals, e.g. a mouse. The extraction of multiple blood
samples allows continuous testing of blood parameters for the
determination of the biological effects induced by the, preferably
human, target antigenxCD3 bispecific single chain antibody of the
invention. Furthermore, the extraction of multiple blood samples
enables the researcher to evaluate the pharmacokinetic profile of
the, preferably human, target antigenxCD3 bispecific single chain
antibody of the invention as defined herein. In addition, potential
side effects, which may be induced by said, preferably human,
target antigenxCD3 bispecific single chain antibody of the
invention reflected in blood parameters can be measured in
different blood samples extracted during the course of the
administration of said antibody. This allows the determination of
the potential toxicity profile of the, preferably human, target
antigenxCD3 bispecific single chain antibody of the invention as
defined herein.
[0094] The advantages of the, preferably human, target antigenxCD3
bispecific single chain antibody of the invention as defined herein
exhibiting cross-species specificity may be briefly summarized as
follows: First, the, preferably human, target antigenxCD3
bispecific single chain antibody of the invention as defined herein
used in preclinical testing is the same as the one used in human
therapy. Thus, it is no longer necessary to develop two independent
molecules, which may differ in their pharmacokinetic properties and
biological activity. This is highly advantageous in that e.g. the
pharmacokinetic results are more directly transferable and
applicable to the human setting than e.g. in conventional surrogate
approaches.
[0095] Second, the uses of the, preferably human, target
antigenxCD3 bispecific single chain antibody of the invention as
defined herein for the preparation of therapeutics in human is less
cost- and labor-intensive than surrogate approaches.
[0096] Third, the, preferably human, target antigenxCD3 bispecific
single chain antibody of the invention as defined herein can be
used for preclinical testing not only in one primate species, but
in a series of different primate species, thereby limiting the risk
of potential species differences between primates and human.
[0097] Fourth, chimpanzee as an endangered species for animal
testing can be avoided if desired.
[0098] Fifth, multiple blood samples can be extracted for extensive
pharmacokinetic studies.
[0099] Sixth, due to the human origin of the, preferably human,
binding molecules according to a preferred embodiment of the
invention, the generation of an immune reaction against said
binding molecules is minimalized when administered to human
patients. Induction of an immune response with antibodies specific
for a drug candidate derived from a non-human species as e.g. a
mouse leading to the development of human-anti-mouse antibodies
(HAMAs) against therapeutic molecules of murine origin is
excluded.
[0100] Last but not least, the therapeutic use of the target
antigenxCD3 bispecific single chain antibody of the invention
provides a novel and inventive therapeutic approach for cancer,
preferably solid tumors, more preferably carcinomas and prostate
cancer.
[0101] As shown in the following examples, the target antigenxCD3
bispecific single chain antibody of the invention provides an
advantageous tool in order to kill target antigen-expressing human
target cells, e.g. cancer cells. Moreover, the cytotoxic activity
of the target antigenxCD3 bispecific single chain antibody of the
invention is higher than the activity of antibodies described in
the art for the exemplified targets.
[0102] It is further preferred for the method of the invention that
the first binding domain capable of binding to an epitope of human
and non-chimpanzee primate CD3.epsilon. chain comprises a VL region
comprising CDR-L1, CDR-L2 and CDR-L3 selected from: (a) CDR-L1 as
depicted in SEQ ID NO. 27, CDR-L2 as depicted in SEQ ID NO. 28 and
CDR-L3 as depicted in SEQ ID NO. 29; [0103] (b) CDR-L1 as depicted
in SEQ ID NO. 117, CDR-L2 as depicted in SEQ ID NO. 118 and CDR-L3
as depicted in SEQ ID NO. 119; and [0104] (c) CDR-L1 as depicted in
SEQ ID NO. 153, CDR-L2 as depicted in SEQ ID NO.
[0105] 154 and CDR-L3 as depicted in SEQ ID NO. 155.
[0106] More preferably, the first binding domain capable of binding
to an epitope of human and non-chimpanzee primate CD3.epsilon.
chain comprises a VL region selected from the group consisting of a
VL region as depicted in SEQ ID NO. 35, 39, 125, 129, 161 or
165.
[0107] It is alternatively preferred for the method of the
invention that the first binding domain capable of binding to an
epitope of human and non-chimpanzee primate CD3.epsilon. chain
comprises a VH region comprising CDR-H 1, CDR-H2 and CDR-H3
selected from:
[0108] (a) CDR-H1 as depicted in SEQ ID NO. 12, CDR-H2 as depicted
in SEQ ID NO. 13 and CDR-H3 as depicted in SEQ ID NO. 14;
[0109] (b) CDR-H1 as depicted in SEQ ID NO. 30, CDR-H2 as depicted
in SEQ ID NO. 31 and CDR-H3 as depicted in SEQ ID NO. 32;
[0110] (c) CDR-H1 as depicted in SEQ ID NO. 48, CDR-H2 as depicted
in SEQ ID NO. 49 and CDR-H3 as depicted in SEQ ID NO. 50;
[0111] (d) CDR-H1 as depicted in SEQ ID NO. 66, CDR-H2 as depicted
in SEQ ID NO. 67 and CDR-H3 as depicted in SEQ ID NO. 68;
[0112] (e) CDR-H1 as depicted in SEQ ID NO. 84, CDR-H2 as depicted
in SEQ ID NO. 85 and CDR-H3 as depicted in SEQ ID NO. 86;
[0113] (f) CDR-H1 as depicted in SEQ ID NO. 102, CDR-H2 as depicted
in SEQ ID NO. 103 and CDR-H3 as depicted in SEQ ID NO. 104;
[0114] (g) CDR-H1 as depicted in SEQ ID NO. 120, CDR-H2 as depicted
in SEQ ID NO. 121 and CDR-H3 as depicted in SEQ ID NO. 122;
[0115] (h) CDR-H1 as depicted in SEQ ID NO. 138, CDR-H2 as depicted
in SEQ ID NO. 139 and CDR-H3 as depicted in SEQ ID NO. 140;
[0116] (i) CDR-H1 as depicted in SEQ ID NO. 156, CDR-H2 as depicted
in SEQ ID NO.
[0117] 157 and CDR-H3 as depicted in SEQ ID NO. 158; and
[0118] (j) CDR-H1 as depicted in SEQ ID NO. 174, CDR-H2 as depicted
in SEQ ID NO.
[0119] 175 and CDR-H3 as depicted in SEQ ID NO. 176.
[0120] More preferably, the binding domain capable of binding to an
epitope of human and non-chimpanzee primate CD3.epsilon. chain
comprises a VH region selected from the group consisting of a VH
region as depicted in SEQ ID NO. 15, 19, 33, 37, 51, 55, 69, 73,
87, 91, 105, 109, 123, 127, 141, 145, 159, 163, 177 or 181.
[0121] It is preferred for the method of the invention that the
first binding domain capable of binding to an epitope of human and
non-chimpanzee primate CD3.epsilon. chain comprises a VL region and
a VH region selected from the group consisting of: [0122] (a) a VL
region as depicted in SEQ ID NO. 17 or 21 and a VH region as
depicted in SEQ ID NO. 15 or 19; [0123] (b) a VL region as depicted
in SEQ ID NO. 35 or 39 and a VH region as depicted in SEQ ID NO. 33
or 37; [0124] (c) a VL region as depicted in SEQ ID NO. 53 or 57
and a VH region as depicted in SEQ ID NO. 51 or 55;
[0125] (d) a VL region as depicted in SEQ ID NO. 71 or 75 and a VH
region as depicted in SEQ ID NO. 69 or 73; [0126] (e) a VL region
as depicted in SEQ ID NO. 89 or 93 and a VH region as depicted in
SEQ ID NO. 87 or 91; [0127] (f) a VL region as depicted in SEQ ID
NO. 107 or 111 and a VH region as depicted in SEQ ID NO. 105 or
109; [0128] (g) a VL region as depicted in SEQ ID NO. 125 or 129
and a VH region as depicted in SEQ ID NO. 123 or 127; [0129] (h) a
VL region as depicted in SEQ ID NO. 143 or 147 and a VH region as
depicted in SEQ ID NO. 141 or 145;
[0130] (i) a VL region as depicted in SEQ ID NO. 161 or 165 and a
VH region as depicted in SEQ ID NO. 159 or 163; and [0131] (j) a VL
region as depicted in SEQ ID NO. 179 or 183 and a VH region as
depicted in SEQ ID NO. 177 or 181.
[0132] More preferably, the first binding domain capable of binding
to an epitope of human and non-chimpanzee primate CD3.epsilon.
chain comprises an amino acid sequence selected from the group
consisting of SEQ ID NOs: 23, 25, 41, 43, 59, 61, 77, 79, 95, 97,
113, 115, 131, 133, 149, 151, 167, 169, 185 or 187.
[0133] As already discussed herein above, it is also preferred for
the method of the invention that also the second binding domain
binds to epitopes/binding sites in the extracellular domain of a
high molecular weight antigen of human and non-chimpanzee
primate.
[0134] In a preferred embodiment of the method of the invention the
second binding domain binds to epitopes/binding sites in the
extracellular domain of c-MET. This target antigen and its
expression characteristics have been described herein above. The
MET tyrosine kinase receptor with an extracellular region of 908 aa
with the following sequential arrangement of independently folded
extracellular domains from membrane-proximal to membrane-distal:
Four Ig domains of together 362 aa (residues 563-924), a
cystein-rich domain of 42 aa (residues 520-561), the beta-chain of
a sema domain of 212 aa (residues 308-519) and the alpha-chain of
the sema domain of 282 aa (residues 25-307). Accordingly, it is
preferred for the method of the invention, that the second binging
domain binds to epitopes/binding sites in the four Ig domains (SEQ
ID NO: 436), a cystein-rich domain (SEQ ID NO: 437), or the
beta-chain of a sema domain (SEQ ID NO: 438) of the extracellular
domain of c-MET, which are all below the 640 aa-threshold.
[0135] In an alternatively preferred embodiment of the method of
the invention the second binding domain binds to epitopes/binding
sites in the extracellular domain of endosialin (TEM1). This target
antigen and its expression characteristics have been described
herein above. For endosialin a extracellular domain consisting of
665 aa and the following sequential arrangement of independently
folded extracellular domains from membrane-proximal to
membrane-distal is described in the art: a mucin domain of 326 aa
(residues 360-685), three EGF-like domains of together 116 aa
(residues 235-350), a Sushi/SCR/CCP domain of 55 aa (residues
176-230) and a C-type lectin domain of 129 aa (residues 29-157).
Accordingly, it is preferred for the method of the invention that
the second binging domain binds to epitopes/binding sites in the
mucin domain (SEQ ID NO: 440), the three EGF-like domains (SEQ ID
NO: 441), or the Sushi/SCR/CCP domain (SEQ ID NO: 442) of the
extracellular domain of TEM1.
[0136] According to a further alternatively preferred embodiment of
the method of the invention the second binding domain binds to
epitopes/binding sites in the extracellular domain of IGF-1R. This
target antigen and its expression characteristics have been
described herein above. For endosialin a extracellular domain
consisting of 905 aa and the following sequential arrangement of
independently folded extracellular domains from membrane-proximal
to membrane-distal is described in the art: three fibronectin type
III domains of together 447 aa (residues 460-906), an L2 domain of
160 aa (residues 300-459), a cystein-rich domain of 149 aa
(residues 151-299) and an L1 domain of 150 aa (residues 1-150).
Accordingly, it is preferred for the method of the invention that
the second binging domain binds to epitopes/binding sites in the
three fibronectin type III domains (SEQ ID NO: 444), and the L2
domain (SEQ ID NO: 445) of the extracellular domain of IGF-1R.
[0137] An alternative embodiment of the invention reltes to a
bispecific single chain antibody comprising a first domain binding
domain capable of binding to CD3 epsilon (CD3.epsilon.) of human
and non-chimpanzee primate and a second domain binding domain
capable of binding to the extracellular domain of the mutated human
PSMA having an amino acid sequence as depicted in SEQ ID NO: 447
but not to the extracellular domain of the rodent PSMA. In other
words, the bispecific antibody of the invention specifically binds
to membrane proximal epitopes, i.e. epitopes formed only by amino
acid resides of the extracellular domain of PSMA, the alpha C-atom
of which has a distance of less than 60 .ANG. from the reference
C-atom (the alpha C-atom of the 13.sup.th aa as counted from the
junction of transmembrane and extracellular region). The specific
superior characteristics of these PSMAxCD3 bispecific single chain
antibodies have been described herein above. Moreover,
corresponding antibodies are exemplified and characterized in the
appended examples.
[0138] It is preferred for the bispecific ingle chain antibody
comprising a first domain binding domain capable of binding to CD3
epsilon (CD3.epsilon.) and a second domain binding domain capable
of binding to the extracellular domain of the mutated human PSMA
having an amino acid sequence as depicted in SEQ ID NO: 447 but not
to the extracellular domain of the rodent PSMA that the first
domain capable of binding to an epitope of human and non-chimpanzee
primate CD3.epsilon. chain comprises an amino acid sequence
selected from the group consisting of SEQ ID NOs: 23, 25, 41, 43,
59, 61, 77, 79, 95, 97, 113, 115, 131, 133, 149, 151, 167, 169, 185
or 187. It is preferred for the bispecific single chain antibodies
that the second domain comprises a VL region comprising CDR-L1,
CDR-L2 and CDR-L3 selected from:
[0139] (a) CDR-L1 as depicted in SEQ ID NO. 269, CDR-L2 as depicted
in SEQ ID NO: 270 and CDR-L3 as depicted in SEQ ID NO. 271;
[0140] (b) CDR-L1 as depicted in SEQ ID NO. 283, CDR-L2 as depicted
in SEQ ID NO: 284 and CDR-L3 as depicted in SEQ ID NO. 285;
[0141] (c) CDR-L1 as depicted in SEQ ID NO. 297, CDR-L2 as depicted
in SEQ ID NO: 298 and CDR-L3 as depicted in SEQ ID NO. 299;
[0142] (d) CDR-L1 as depicted in SEQ ID NO. 311, CDR-L2 as depicted
in SEQ ID NO: 312 and CDR-L3 as depicted in SEQ ID NO. 313;
[0143] (e) CDR-L1 as depicted in SEQ ID NO. 325, CDR-L2 as depicted
in SEQ ID NO. 326 and CDR-L3 as depicted in SEQ ID NO. 327;
[0144] (f) CDR-L1 as depicted in SEQ ID NO. 255, CDR-L2 as depicted
in SEQ ID NO.
[0145] 256 and CDR-L3 as depicted in SEQ ID NO. 257; and
[0146] (g) CDR-L1 as depicted in SEQ ID NO. 481, CDR-L2 as depicted
in SEQ ID NO. 482 and CDR-L3 as depicted in SEQ ID NO. 483.
[0147] It is also preferred for the bispecific single chain
antibodies of the invention that the second domain comprises a VH
region comprising CDR-H1, CDR-H2 and CDR-H3 selected from: [0148]
(a) CDR-H1 as depicted in SEQ ID NO. 274, CDR-H2 as depicted in SEQ
ID NO:
[0149] 275 and CDR-H3 as depicted in SEQ ID NO. 276; [0150] (b)
CDR-H1 as depicted in SEQ ID NO. 288, CDR-H2 as depicted in SEQ ID
NO:
[0151] 289 and CDR-H3 as depicted in SEQ ID NO. 290; [0152] (c)
CDR-H1 as depicted in SEQ ID NO. 302, CDR-H2 as depicted in SEQ ID
NO:
[0153] 303 and CDR-H3 as depicted in SEQ ID NO. 304; [0154] (d)
CDR-H1 as depicted in SEQ ID NO. 316, CDR-H2 as depicted in SEQ ID
NO: 317 and CDR-H3 as depicted in SEQ ID NO. 318;
[0155] (e) CDR-H1 as depicted in SEQ ID NO. 330, CDR-H2 as depicted
in SEQ ID NO:
[0156] 331 and CDR-H3 as depicted in SEQ ID NO. 332; [0157] (f)
CDR-H1 as depicted in SEQ ID NO. 260, CDR-H2 as depicted in SEQ ID
NO:
[0158] 261 and CDR-H3 as depicted in SEQ ID NO. 262; and [0159] (g)
CDR-H1 as depicted in SEQ ID NO. 476, CDR-H2 as depicted in SEQ ID
NO:
[0160] 477 and CDR-H3 as depicted in SEQ ID NO. 478.
[0161] In a further preferred embodiment of a bispecific single
chain antibody of the invention the second domain comprises a VL
region and a VH region selected from the group consisting of:
[0162] (a) a VL region as depicted in SEQ ID NO. 268 and a VH
region as depicted in SEQ ID NO. 273; [0163] (b) a VL region as
depicted in SEQ ID NO. 282 and a VH region as depicted in SEQ ID
NO. 287;
[0164] (c) a VL region as depicted in SEQ ID NO. 296 and a VH
region as depicted in SEQ ID NO. 301; [0165] (d) a VL region as
depicted in SEQ ID NO. 310 and a VH region as depicted in SEQ ID
NO. 315; [0166] (e) a VL region as depicted in SEQ ID NO. 324 and a
VH region as depicted in SEQ ID NO. 329; [0167] (f) a VL region as
depicted in SEQ ID NO. 254 and a VH region as depicted in SEQ ID
NO. 259; and [0168] (g) a VL region as depicted in SEQ ID NO. 480
and a VH region as depicted in SEQ ID NO. 475.
[0169] More preferably, the second domain comprises an amino acid
sequence selected from the group consisting of SEQ ID NOs: 278,
292, 306, 320, 334, 485 or 264. It is preferred for the bispecific
single chain antibody comprising a first domain binding domain
capable of binding to CD3 epsilon (CD3.epsilon.) of human and
non-chimpanzee primate and a second domain binding domain capable
of binding to the extracellular domain of the mutated human PSMA
chimera that the first domain capable of binding to an epitope of
human and non-chimpanzee primate CD3.epsilon. chain comprises an
amino acid sequence selected from the group consisting of SEQ ID
NOs: 23, 25, 41, 43, 59, 61, 77, 79, 95, 97, 113, 115, 131, 133,
149, 151, 167, 169, 185 or 187.
[0170] A particularly preferred embodiment of the invention
concerns an above characterized polypeptide, wherein the bispecific
single chain antibody molecule comprises a sequence selected from:
[0171] (a) an amino acid sequence as depicted in any of SEQ ID NOs.
280, 294, 308, 322, 336, 266 or 487; [0172] (b) an amino acid
sequence encoded by a nucleic acid sequence as depicted in any of
SEQ ID NOs: 281, 295, 309, 267, 323, 337 or 488; and [0173] (c) an
amino acid sequence at least 90% identical, more preferred at least
95% identical, most preferred at least 96% identical to the amino
acid sequence of (a) or (b).
[0174] The invention relates to a bispecific single chain antibody
molecule comprising an amino acid sequence as depicted in any of
SEQ ID NOs: 280, 294, 266, 308, 322, 336 or 487, as well as to an
amino acid sequences at least 85% identical, preferably 90%, more
preferred at least 95% identical, most preferred at least 96, 97,
98, or 99% identical to the amino acid sequence of SEQ ID NOs: 280,
294, 266, 308, 322, 336 or 487. The invention relates also to the
corresponding nucleic acid sequences as depicted in any of SEQ ID
NOs: 281, 295, 267, 309, 323, 337 or 488, as well as to nucleic
acid sequences at least 85% identical, preferably 90%, more
preferred at least 95% identical, most preferred at least 96, 97,
98, or 99% identical to the nucleic acid sequences shown in SEQ ID
NOs: 281, 295, 267, 309, 323, 337 or 488. Preferred domain
arrangements in the PSMAxCD3 bispecific single chain antibody
constructs of the invention are shown in the following
examples.
[0175] In a preferred embodiment of the invention, the bispecific
single chain antibodies are cross-species specific for CD3 epsilon
and for the human and non-chimpanzee primate cell surface antigen
PSMA, recognized by their second binding domain.
[0176] In an alternative embodiemt the invention provides a
bispecific single chain antibody comprising a first domain binding
domain capable of binding to CD3 epsilon (CD3.epsilon.) of human
and non-chimpanzee primate and a second domain binding domain
capable of binding to the extracellular domain of the mutated human
FAP.alpha. chimera having an amino acid sequence as depicted in SEQ
ID NO: 448 but not to the extracellular domain of the rodent
FAP.alpha.. In other words, the bispecific antibody of the
invention specifically binds to membrane proximal epitopes, i.e.
epitopes formed only by amino acid resides of the extracellular
domain of FAP.alpha., the alpha C-atom of which has a distance of
less than 60 .ANG. from the reference C-atom (the alpha C-atom of
the 13.sup.th aa as counted from the junction of transmembrane and
extracellular region).
[0177] According to a preferred embodiment of the invention an
above characterized bispecific single chain antibody molecule
comprises a group of the following sequences as CDR H1, CDR H2, CDR
H3, CDR L1, CDR L2 and CDR L3 in the second binding domain selected
from: CDR H1-3 of SEQ ID NO: 1137-1139 and CDR L1-3 of SEQ ID NO:
1132-1134.
[0178] The sequences of the corresponding VL- and VH-regions of the
second binding domain of the bispecific single chain antibody
molecule of the invention as well as of the respective scFvs are
shown in the sequence listing.
[0179] According to a preferred embodiment of the invention an
above characterized bispecific single chain antibody molecule
comprises a group of the following sequences as CDR H1, CDR H2, CDR
H3, CDR L1, CDR L2 and CDR L3 in the second binding domain selected
from the group consisting of:
[0180] a) CDR H1-3 of SEQ ID NO: 808-810 and CDR L1-3 of SEQ ID NO:
-813-815;
[0181] b) CDR H1-3 of SEQ ID NO: 794-796 and CDR L1-3 of SEQ ID NO:
799-801, [0182] c) CDR H1-3 of SEQ ID NO: 738-740 and CDR L1-3 of
SEQ ID NO: 743-745; [0183] d) CDR H1-3 of SEQ ID NO: 752-754 and
CDR L1-3 of SEQ ID NO: 757-759; [0184] e) CDR H1-3 of SEQ ID NO:
822-824 and CDR L1-3 of SEQ ID NO: 827-829; [0185] f) CDR H1-3 of
SEQ ID NO: 766-768 and CDR L1-3 of SEQ ID NO: 771-773; and [0186]
g) CDR H1-3 of SEQ ID NO: 780-782 and CDR L1-3 of SEQ ID NO:
785-787.
[0187] In the bispecific single chain antibody molecule of the
invention the binding domains are arranged in the order
VL-VH--VH-VL, VL-VH-VL-VH, VH-VL-VH-VL or VH-VL-VL-VH, as
exemplified in the appended examples. Preferably, the binding
domains are arranged in the order VH FAP alpha-VL FAP alpha-VH
CD3-VL CD3 or VL FAP alpha-VH FAP alpha-VH CD3-VL CD3. More
preferred, the binding domains are arranged in the order VL FAP
alpha-VH FAP alpha-VH CD3-VL CD3.
[0188] It is preferred for the bispecific single chain antibody
comprising a first domain binding domain capable of binding to CD3
epsilon (CD3.epsilon.) of human and non-chimpanzee primate and a
second domain binding domain capable of binding to the
extracellular domain of the mutated human FAP.alpha. chimera that
the first domain capable of binding to an epitope of human and
non-chimpanzee primate CD3.epsilon. chain comprises an amino acid
sequence selected from the group consisting of SEQ ID NOs: 23, 25,
41, 43, 59, 61, 77, 79, 95, 97, 113, 115, 131, 133, 149, 151, 167,
169, 185 or 187.
[0189] A particularly preferred embodiment of the invention
concerns an above characterized polypeptide, wherein the bispecific
single chain antibody molecule comprises a sequence selected from:
[0190] (a) an amino acid sequence as depicted in any of SEQ ID NOs.
819, 805, 749, 763, 833, 777 or 791; [0191] (b) an amino acid
sequence encoded by a nucleic acid sequence as depicted in any of
SEQ ID NOs: 820, 806, 750, 764, 834, 778 or 792; and [0192] (c) an
amino acid sequence at least 90% identical, more preferred at least
95%) identical, most preferred at least 96% identical to the amino
acid sequence of (a) or (b).
[0193] The invention relates to a bispecific single chain antibody
molecule comprising an amino acid sequence as depicted in any of
SEQ ID NOs: 819, 805, 749, 763, 833, 777 or 791, as well as to an
amino acid sequences at least 85% identical, preferably 90%, more
preferred at least 95% identical, most preferred at least 96, 97,
98, or 99%) identical to the amino acid sequence of SEQ ID NOs:
819, 805, 749, 763, 833, 777 or 791. The invention relates also to
the corresponding nucleic acid sequences as depicted in any of SEQ
ID NOs: 820, 806, 750, 764, 834, 778 or 792, as well as to nucleic
acid sequences at least 85% identical, preferably 90%, more
preferred at least 95% identical, most preferred at least 96, 97,
98, or 99% identical to the nucleic acid sequences shown in SEQ ID
NOs: 820, 806, 750, 764, 834, 778 or 792. Preferred domain
arrangements in the FAPaxCD3 bispecific single chain antibody
constructs of the invention are shown in the following
examples.
[0194] In a further alternative embodiement the invention provides
a bispecific single chain antibody comprising a first domain
binding domain capable of binding to CD3 epsilon (CD3.epsilon.) of
human and non-chimpanzee primate and a second domain binding domain
capable of binding to the four Ig domains (SEQ ID NO: 436), a
cystein-rich domain (SEQ ID NO: 437), or the beta-chain of a sema
domain (SEQ ID NO: 438) of the extracellular domain of c-MET.
[0195] According to a preferred embodiment of the invention an
above characterized bispecific single chain antibody molecule
comprises a group of the following sequences as CDR H1, CDR H2, CDR
H3, CDR L1, CDR L2 and CDR L3 in the second binding domain selected
from the group consisting of:
[0196] a) CDR H1-3 of SEQ ID NO: -500-502 and CDR L1-3 of SEQ ID
NO: -505-507;
[0197] b) CDR H1-3 of SEQ ID NO: 514-516 and CDR L1-3 of SEQ ID NO:
519-521; [0198] c) CDR H1-3 of SEQ ID NO: 528-530 and CDR L1-3 of
SEQ ID NO: 533-535; [0199] d) CDR H1-3 of SEQ ID NO: 542-544 and
CDR L1-3 of SEQ ID NO: 547-549;
[0200] e) CDR H1-3 of SEQ ID NO: 556-558 and CDR L1-3 of SEQ ID NO:
561-563;
[0201] f) CDR H1-3 of SEQ ID NO: 570-572 and CDR L1-3 of SEQ ID NO:
575-577;
[0202] g) CDR H1-3 of SEQ ID NO: 584-586 and CDR L1-3 of SEQ ID NO:
589-591; [0203] h) CDR H1-3 of SEQ ID NO: 598-600 and CDR L1-3 of
SEQ ID NO: 603-605; [0204] i) CDR H1-3 of SEQ ID NO: 612-614 and
CDR L1-3 of SEQ ID NO: 617-619;
[0205] j) CDR H1-3 of SEQ ID NO: 626-628 and CDR L1-3 of SEQ ID NO:
631-633;
[0206] k) CDR H1-3 of SEQ ID NO: 640-642 and CDR L1-3 of SEQ ID NO:
645-647; [0207] I) CDR H1-3 of SEQ ID NO: 654-656 and CDR L1-3 of
SEQ ID NO: 659-661; [0208] m) CDR H1-3 of SEQ ID NO: 668-670 and
CDR L1-3 of SEQ ID NO: 673-675; [0209] n) CDR H1-3 of SEQ ID NO:
682-684 and CDR L1-3 of SEQ ID NO: 687-689; [0210] o) CDR H1-3 of
SEQ ID NO: 696-698 and CDR L1-3 of SEQ ID NO: 701-703; [0211] p)
CDR H1-3 of SEQ ID NO: 710-712 and CDR L1-3 of SEQ ID NO: 715-717;
and [0212] q) CDR H1-3 of SEQ ID NO: 724-726 and CDR L1-3 of SEQ ID
NO: 729-731.
[0213] The sequences of the corresponding VL- and VH-regions of the
second binding domain of the bispecific single chain antibody
molecule of the invention as well as of the respective scFvs are
shown in the sequence listing.
[0214] In the bispecific single chain antibody molecule of the
invention the binding domains are arranged in the order
VL-VH--VH-VL, VL-VH-VL-VH, VH-VL-VH-VL or VH-VL-VL-VH, as
exemplified in the appended examples. Preferably, the binding
domains are arranged in the order VH C-MET-VL C-MET-VH CD3-VL CD3
or VL C-MET-VH C-MET-VH CD3-VL CD3.
[0215] More preferably, the first domain capable of binding to an
epitope of human and non-chimpanzee primate CD3.epsilon. chain
comprises an amino acid sequence selected from the group consisting
of SEQ ID NOs: 23, 25, 41, 43, 59, 61, 77, 79, 95, 97, 113, 115,
131, 133, 149, 151, 167, 169, 185 or 187.
[0216] A particularly preferred embodiment of the invention
concerns an above characterized polypeptide, wherein the bispecific
single chain antibody molecule comprises a sequence selected
from:
[0217] (a) an amino acid sequence as depicted in any of SEQ ID NOs.
511, 525, 539, 553, 567 or 581;
[0218] (b) an amino acid sequence encoded by a nucleic acid
sequence as depicted in any of SEQ ID NOs: 512, 526, 540, 554, 568
or 582; and
[0219] (c) an amino acid sequence at least 90% identical, more
preferred at least 95% identical, most preferred at least 96%
identical to the amino acid sequence of (a) or (b).
[0220] The invention relates to a bispecific single chain antibody
molecule comprising an amino acid sequence as depicted in any of
SEQ ID NOs: 511, 525, 539, 553, 567 or 581, as well as to an amino
acid sequences at least 85% identical, preferably 90%, more
preferred at least 95% identical, most preferred at least 96, 97,
98, or 99%) identical to the amino acid sequence of SEQ ID NOs:
511, 525, 539, 553, 567 or 581.
[0221] The invention relates also to the corresponding nucleic acid
sequences as depicted in any of SEQ ID NOs: 512, 526, 540, 554, 568
or 582 as well as to nucleic acid sequences at least 85% identical,
preferably 90%, more preferred at least 95% identical, most
preferred at least 96, 97, 98, or 99% identical to the nucleic acid
sequences shown in SEQ ID NOs: 512, 526, 540, 554, 568 or 582.
[0222] Preferred domain arrangements in the c-METxCD3 bispecific
single chain antibody constructs of the invention are shown in the
following examples.
[0223] According to an alternative embodiment the invention
provides a bispecific single chain antibody comprising a first
domain binding domain capable of binding to CD3 epsilon
(CD3.epsilon.) of human and non-chimpanzee primate and a second
domain binding domain capable of binding to the mucin domain (SEQ
ID NO: 440), the three EGF-like domains (SEQ ID NO: 441), or the
Sushi/SCR/CCP domain (SEQ ID NO: 442) of the extracellular domain
of endosialin (TEM1).
[0224] Preferably the first domain capable of binding to an epitope
of human and non-chimpanzee primate CD3.epsilon. chain comprises an
amino acid sequence selected from the group consisting of SEQ ID
NOs: 23, 25, 41, 43, 59, 61, 77, 79, 95, 97, 113, 115, 131, 133,
149, 151, 167, 169, 185 or 187.
[0225] Moreover, in an alternative embodiment the invention
provides a bispecific single chain antibody comprising a first
domain binding domain capable of binding to CD3 epsilon
(CD3.epsilon.) of human and non-chimpanzee primate and a second
domain binding domain capable of binding to the three fibronectin
type III domains (SEQ ID NO: 444), the L2 domain (SEQ ID NO: 445)
of the extracellular domain of IGF-1R.
[0226] According to a preferred embodiment of the invention an
above characterized bispecific single chain antibody molecule
comprises a group of the following sequences as CDR H1, CDR H2, CDR
H3, CDR L1, CDR L2 and CDR L3 in the second binding domain selected
from the group consisting of: [0227] a) CDR H1-3 of SEQ ID NO:
-836-838 and CDR L1-3 of SEQ ID NO: -841-843; and [0228] b) CDR
H1-3 of SEQ ID NO: 850-852 and CDR L1-3 of SEQ ID NO: 855-857.
[0229] The sequences of the corresponding VL- and VH-regions of the
second binding domain of the bispecific single chain antibody
molecule of the invention as well as of the respective scFvs are
shown in the sequence listing.
[0230] In the bispecific single chain antibody molecule of the
invention the binding domains are arranged in the order
VL-VH--VH-VL, VL-VH-VL-VH, VH-VL-VH-VL or VH-VL-VL-VH, as
exemplified in the appended examples. Preferably, the binding
domains are arranged in the order VH IGF-1R-VL IGF-1R-VH CD3-VL CD3
or VL IGF-1R-VH IGF-1R-VH CD3-VL CD3.
[0231] Preferably, the first domain capable of binding to an
epitope of human and non-chimpanzee primate CD3.epsilon. chain
comprises an amino acid sequence selected from the group consisting
of SEQ ID NOs: 23, 25, 41, 43, 59, 61, 77, 79, 95, 97, 113, 115,
131, 133, 149, 151, 167, 169, 185 or 187.
[0232] A particularly preferred embodiment of the invention
concerns an above characterized polypeptide, wherein the bispecific
single chain antibody molecule comprises a sequence selected
from:
[0233] (a) an amino acid sequence as depicted in any of SEQ ID NOs:
847 or 861;
[0234] (b) an amino acid sequence encoded by a nucleic acid
sequence as depicted in any of SEQ ID NOs: 848, or 862; and
[0235] (c) an amino acid sequence at least 90% identical, more
preferred at least 95% identical, most preferred at least 96%
identical to the amino acid sequence of (a) or (b).
[0236] The invention relates to a bispecific single chain antibody
molecule comprising an amino acid sequence as depicted in any of
SEQ ID NOs: 847 or 861, as well as to an amino acid sequences at
least 85% identical, preferably 90%, more preferred at least 95%
identical, most preferred at least 96, 97, 98, or 99% identical to
the amino acid sequence of SEQ ID NOs: 847 or 861. The invention
relates also to the corresponding nucleic acid sequences as
depicted in any of SEQ ID NOs: 848, or 862 as well as to nucleic
acid sequences at least 85% identical, preferably 90%, more
preferred at least 95% identical, most preferred at least 96, 97,
98, or 99%) identical to the nucleic acid sequences shown in SEQ ID
NOs: 848, or 862. Preferred domain arrangements in the IGF-1RxCD3
bispecific single chain antibody constructs of the invention are
shown in the following examples.
[0237] The invention relates to bispecific single chain antibody
molecule comprising the above identified amino acid sequences, as
well as to amino acid sequences at least 85% identical, preferably
90%, more preferred at least 95% identical, most preferred at least
96, 97, 98, or 99% identical to the amino acid sequence of said
sequences. As described herein above, the specificity of an
antibody is generally understood to be determined by the CDR
sequences. Accordingly, in order to maintain the specificity of a
given group of CDRs, e.g three CDRs of a heavy chain and three CDRs
of a light chain, the sequence of these CDRs has to be conserved.
Accordingly variants of bispecific single antibodies as identified
herein, which also fall under the present invention are preferably
variants having more than one amino acid substituions in FR regions
instead of the CDRs. It is to be understood that the sequence
identity is determined over the entire nucleotide or amino acid
sequence. For sequence alignments, for example, the programs Gap or
BestFit can be used (Needleman and Wunsch J. Mol. Biol. 48 (1970),
443-453; Smith and Waterman, Adv. Appl. Math 2 (1981), 482-489),
which is contained in the GCG software package (Genetics Computer
Group, 575 Science Drive, Madison, Wis., USA 53711 (1991). It is a
routine method for those skilled in the art to determine and
identify a nucleotide or amino acid sequence having e.g. 85% (90%,
95%, 96%, 97%, 98% or 99%) sequence identity to the nucleotide or
amino acid sequences of the bispecific single single chain antibody
of the invention by using e.g. one of the above mentioned programs.
For example, according to Crick's Wobble hypothesis, the 5' base on
the anti-codon is not as spatially confined as the other two bases,
and could thus have non-standard base pairing. Put in other words:
the third position in a codon triplet may vary so that two triplets
which differ in this third position may encode the same amino acid
residue. Said hypothesis is well known to the person skilled in the
art (see e.g. http://en.wikipedia.org/wiki/Wobble_Hypothesis;
Crick, J Mol Biol 19 (1966): 548-55).
[0238] In an alternative embodiment the present invention provides
a nucleic acid sequence encoding an above described bispecific
single chain antibody molecule of the invention.
[0239] The present invention also relates to a vector comprising
the nucleic acid molecule of the present invention.
[0240] Many suitable vectors are known to those skilled in
molecular biology, the choice of which would depend on the function
desired and include plasmids, cosmids, viruses, bacteriophages and
other vectors used conventionally in genetic engineering. Methods
which are well known to those skilled in the art can be used to
construct various plasmids and vectors; see, for example, the
techniques described in Sambrook et al. (loc cit.) and Ausubel,
Current Protocols in Molecular Biology, Green Publishing Associates
and Wiley Interscience, N.Y. (1989), (1994). Alternatively, the
polynucleotides and vectors of the invention can be reconstituted
into liposomes for delivery to target cells. As discussed in
further details below, a cloning vector was used to isolate
individual sequences of DNA. Relevant sequences can be transferred
into expression vectors where expression of a particular
polypeptide is required. Typical cloning vectors include
pBluescript SK, pGEM, pUC9, pBR322 and pGBT9. Typical expression
vectors include pTRE, pCAL-n-EK, pESP-1, pOP13CAT.
[0241] Preferably said vector comprises a nucleic acid sequence
which is a regulatory sequence operably linked to said nucleic acid
sequence defined herein.
[0242] The term "regulatory sequence" refers to DNA sequences,
which are necessary to effect the expression of coding sequences to
which they are ligated. The nature of such control sequences
differs depending upon the host organism. In prokaryotes, control
sequences generally include promoter, ribosomal binding site, and
terminators. In eukaryotes generally control sequences include
promoters, terminators and, in some instances, enhancers,
transactivators or transcription factors. The term "control
sequence" is intended to include, at a minimum, all components the
presence of which are necessary for expression, and may also
include additional advantageous components.
[0243] The term "operably linked" refers to a juxtaposition wherein
the components so described are in a relationship permitting them
to function in their intended manner. A control sequence "operably
linked" to a coding sequence is ligated in such a way that
expression of the coding sequence is achieved under conditions
compatible with the control sequences. In case the control sequence
is a promoter, it is obvious for a skilled person that
double-stranded nucleic acid is preferably used.
[0244] Thus, the recited vector is preferably an expression vector.
An "expression vector" is a construct that can be used to transform
a selected host and provides for expression of a coding sequence in
the selected host. Expression vectors can for instance be cloning
vectors, binary vectors or integrating vectors. Expression
comprises transcription of the nucleic acid molecule preferably
into a translatable mRNA. Regulatory elements ensuring expression
in prokaryotes and/or eukaryotic cells are well known to those
skilled in the art. In the case of eukaryotic cells they comprise
normally promoters ensuring initiation of transcription and
optionally poly-A signals ensuring termination of transcription and
stabilization of the transcript. Possible regulatory elements
permitting expression in prokaryotic host cells comprise, e.g., the
P.sub.L, lac, trp or tac promoter in E. coli, and examples of
regulatory elements permitting expression in eukaryotic host cells
are the AOX1 or GAL1 promoter in yeast or the CMV-, SV40-,
RSV-promoter (Rous sarcoma virus), CMV-enhancer, SV40-enhancer or a
globin intron in mammalian and other animal cells.
[0245] Beside elements, which are responsible for the initiation of
transcription such regulatory elements may also comprise
transcription termination signals, such as the SV40-poly-A site or
the tk-poly-A site, downstream of the polynucleotide. Furthermore,
depending on the expression system used leader sequences capable of
directing the polypeptide to a cellular compartment or secreting it
into the medium may be added to the coding sequence of the recited
nucleic acid sequence and are well known in the art; see also the
appended Examples. The leader sequence(s) is (are) assembled in
appropriate phase with translation, initiation and termination
sequences, and preferably, a leader sequence capable of directing
secretion of translated protein, or a portion thereof, into the
periplasmic space or extracellular medium. Optionally, the
heterologous sequence can encode a fusion protein including an
N-terminal identification peptide imparting desired
characteristics, e.g., stabilization or simplified purification of
expressed recombinant product; see supra. In this context, suitable
expression vectors are known in the art such as Okayama-Berg cDNA
expression vector pcDV1 (Pharmacia), pCDM8, pRc/CMV, pcDNA1, pcDNA3
(In-vitrogene), pEF-DHFR, pEF-ADA or pEF-neo (Mack et al. PNAS
(1995) 92, 7021-7025 and Raum et al. Cancer Immunol Immunother
(2001) 50(3), 141-150) or pSPORT1 (GIBCO BRL).
[0246] Preferably, the expression control sequences will be
eukaryotic promoter systems in vectors capable of transforming of
transfecting eukaryotic host cells, but control sequences for
prokaryotic hosts may also be used. Once the vector has been
incorporated into the appropriate host, the host is maintained
under conditions suitable for high level expression of the
nucleotide sequences, and as desired, the collection and
purification of the bispecific single chain antibody molecule of
the invention may follow; see, e.g., the appended examples.
[0247] An alternative expression system, which can be used to
express a cell cycle interacting protein is an insect system. In
one such system, Autographa californica nuclear polyhedrosis virus
(AcNPV) is used as a vector to express foreign genes in Spodoptera
frugiperda cells or in Trichoplusia larvae. The coding sequence of
a recited nucleic acid molecule may be cloned into a nonessential
region of the virus, such as the polyhedrin gene, and placed under
control of the polyhedrin promoter. Successful insertion of said
coding sequence will render the polyhedrin gene inactive and
produce recombinant virus lacking coat protein coat. The
recombinant viruses are then used to infect S. frugiperda cells or
Trichoplusia larvae in which the protein of the invention is
expressed (Smith, J. Virol. 46 (1983), 584; Engelhard, Proc. Nat.
Acad. Sci. USA 91 (1994), 3224-3227).
[0248] Additional regulatory elements may include transcriptional
as well as translational enhancers. Advantageously, the
above-described vectors of the invention comprise a selectable
and/or scorable marker.
[0249] Selectable marker genes useful for the selection of
transformed cells and, e.g., plant tissue and plants are well known
to those skilled in the art and comprise, for example,
antimetabolite resistance as the basis of selection for dhfr, which
confers resistance to methotrexate (Reiss, Plant Physiol. (Life
Sci. Adv.) 13 (1994), 143-149);
[0250] npt, which confers resistance to the aminoglycosides
neomycin, kanamycin and paromycin (Herrera-Estrella, EMBO J. 2
(1983), 987-995) and hygro, which confers resistance to hygromycin
(Marsh, Gene 32 (1984), 481-485). Additional selectable genes have
been described, namely trpB, which allows cells to utilize indole
in place of tryptophan; hisD, which allows cells to utilize
histinol in place of histidine (Hartman, Proc. Natl. Acad. Sci. USA
85 (1988), 8047); mannose-6-phosphate isomerase which allows cells
to utilize mannose (WO 94/20627) and ODC (ornithine decarboxylase)
which confers resistance to the ornithine decarboxylase inhibitor,
2-(difluoromethyl)-DL-ornithine, DFMO (McConlogue, 1987, In:
Current Communications in Molecular Biology, Cold Spring Harbor
Laboratory ed.) or deaminase from Aspergillus terreus which confers
resistance to Blasticidin S (Tamura, Biosci. Biotechnol. Biochem.
59 (1995), 2336-2338).
[0251] Useful scorable markers are also known to those skilled in
the art and are commercially available. Advantageously, said marker
is a gene encoding luciferase (Giacomin, Pl. Sci. 116 (1996),
59-72; Scikantha, J. Bact. 178 (1996), 121), green fluorescent
protein (Gerdes, FEBS Lett. 389 (1996), 44-47) or
.beta.-glucuronidase (Jefferson, EMBO J. 6 (1987), 3901-3907). This
embodiment is particularly useful for simple and rapid screening of
cells, tissues and organisms containing a recited vector.
[0252] As described above, the recited nucleic acid molecule can be
used alone or as part of a vector to express the bispecific single
chain antibody molecule of the invention in cells, for, e.g.,
purification but also for gene therapy purposes. The nucleic acid
molecules or vectors containing the DNA sequence(s) encoding any
one of the above described bispecific single chain antibody
molecule of the invention is introduced into the cells which in
turn produce the polypeptide of interest. Gene therapy, which is
based on introducing therapeutic genes into cells by ex-vivo or
in-vivo techniques is one of the most important applications of
gene transfer. Suitable vectors, methods or gene-delivery systems
for in-vitro or in-vivo gene therapy are described in the
literature and are known to the person skilled in the art; see,
e.g., Giordano, Nature Medicine 2 (1996), 534-539; Schaper, Circ.
Res. 79 (1996), 911-919; Anderson, Science 256 (1992), 808-813;
Verma, Nature 389 (1994), 239; Isner, Lancet 348 (1996), 370-374;
Muhlhauser, Circ. Res. 77 (1995), 1077-1086; Onodera, Blood 91
(1998), 30-36; Verma, Gene Ther. 5 (1998), 692-699; Nabel, Ann.
N.Y. Acad. Sci. 811 (1997), 289-292; Verzeletti, Hum. Gene Ther. 9
(1998), 2243-51; Wang, Nature Medicine 2 (1996), 714-716; WO
94/29469; WO 97/00957, U.S. Pat. No. 5,580,859; U.S. Pat. No.
5,589,466; or Schaper, Current Opinion in Biotechnology 7 (1996),
635-640; dos Santos Coura and Nardi Virol J. (2007), 4:99. The
recited nucleic acid molecules and vectors may be designed for
direct introduction or for introduction via liposomes, or viral
vectors (e.g., adenoviral, retroviral) into the cell. Preferably,
said cell is a germ line cell, embryonic cell, or egg cell or
derived there from, most preferably said cell is a stem cell. An
example for an embryonic stem cell can be, inter alia, a stem cell
as described in Nagy, Proc. Natl. Acad. Sci. USA 90 (1993),
8424-8428.
[0253] The invention also provides for a host transformed or
transfected with a vector of the invention. Said host may be
produced by introducing the above described vector of the invention
or the above described nucleic acid molecule of the invention into
the host. The presence of at least one vector or at least one
nucleic acid molecule in the host may mediate the expression of a
gene encoding the above described single chain antibody
constructs.
[0254] The described nucleic acid molecule or vector of the
invention, which is introduced in the host may either integrate
into the genome of the host or it may be maintained
extrachromosomally.
[0255] The host can be any prokaryote or eukaryotic cell.
[0256] The term "prokaryote" is meant to include all bacteria,
which can be transformed or transfected with DNA or RNA molecules
for the expression of a protein of the invention. Prokaryotic hosts
may include gram negative as well as gram positive bacteria such
as, for example, E. coli, S. typhimurium, Serratia marcescens and
Bacillus subtilis. The term "eukaryotic" is meant to include yeast,
higher plant, insect and preferably mammalian cells. Depending upon
the host employed in a recombinant production procedure, the
protein encoded by the polynucleotide of the present invention may
be glycosylated or may be non-glycosylated. Especially preferred is
the use of a plasmid or a virus containing the coding sequence of
the bispecific single chain antibody molecule of the invention and
genetically fused thereto an N-terminal FLAG-tag and/or C-terminal
His-tag. Preferably, the length of said FLAG-tag is about 4 to 8
amino acids, most preferably 8 amino acids. An above described
polynucleotide can be used to transform or transfect the host using
any of the techniques commonly known to those of ordinary skill in
the art. Furthermore, methods for preparing fused, operably linked
genes and expressing them in, e.g., mammalian cells and bacteria
are well-known in the art (Sambrook, loc cit.).
[0257] Preferably, said the host is a bacterium or an insect,
fungal, plant or animal cell.
[0258] It is particularly envisaged that the recited host may be a
mammalian cell. Particularly preferred host cells comprise CHO
cells, COS cells, myeloma cell lines like SP2/0 or NS/0. As
illustrated in the appended examples, particularly preferred are
CHO-cells as hosts.
[0259] More preferably said host cell is a human cell or human cell
line, e.g. per.c6 (Kroos, Biotechnol. Prog., 2003, 19:163-168).
[0260] In a further embodiment, the present invention thus relates
to a process for the production of a bispecific single chain
antibody molecule of the invention, said process comprising
culturing a host of the invention under conditions allowing the
expression of the bispecific single chain antibody molecule of the
invention and recovering the produced polypeptide from the
culture.
[0261] The transformed hosts can be grown in fermentors and
cultured according to techniques known in the art to achieve
optimal cell growth. The bispecific single chain antibody molecule
of the invention can then be isolated from the growth medium,
cellular lysates, or cellular membrane fractions. The isolation and
purification of the, e.g., microbially expressed bispecific single
chain antibody molecules may be by any conventional means such as,
for example, preparative chromatographic separations and
immunological separations such as those involving the use of
monoclonal or polyclonal antibodies directed, e.g., against a tag
of the bispecific single chain antibody molecule of the invention
or as described in the appended examples.
[0262] The conditions for the culturing of a host, which allow the
expression are known in the art to depend on the host system and
the expression system/vector used in such process. The parameters
to be modified in order to achieve conditions allowing the
expression of a recombinant polypeptide are known in the art. Thus,
suitable conditions can be determined by the person skilled in the
art in the absence of further inventive input.
[0263] Once expressed, the bispecific single chain antibody
molecule of the invention can be purified according to standard
procedures of the art, including ammonium sulfate precipitation,
affinity columns, column chromatography, gel electrophoresis and
the like; see, Scopes, "Protein Purification", Springer-Verlag,
N.Y. (1982). Substantially pure polypeptides of at least about 90
to 95% homogeneity are preferred, and 98 to 99% or more homogeneity
are most preferred, for pharmaceutical uses. Once purified,
partially or to homogeneity as desired, the bispecific single chain
antibody molecule of the invention may then be used therapeutically
(including extracorporeally) or in developing and performing assay
procedures. Furthermore, examples for methods for the recovery of
the bispecific single chain antibody molecule of the invention from
a culture are described in detail in the appended examples.
[0264] Furthermore, the invention provides for a composition
comprising a bispecific single chain antibody molecule of the
invention or a bispecific single chain antibody as produced by the
process disclosed above. Preferably, said composition is a
pharmaceutical composition.
[0265] The invention provides also for a bispecific single chain
antibody molecule as defined herein, or produced according to the
process as defined herein, wherein said bispecific single chain
antibody molecule is for use in the prevention, treatment or
amelioration of cancer. Preferably, said cancer is a solid tumor,
more preferably a carcinoma or prostate cancer. It is preferred
that the bispecific single chain is further comprising suitable
formulations of carriers, stabilizers and/or excipients. Moreover,
it is preferred that said bispecific single chain antibody molecule
is suitable to be administered in combination with an additional
drug. Said drug may be a non-proteinaceous compound or a
proteinaceous compound and may be administered simultaneously or
non-simultaneously with the bispecific single chain antibody
molecule as defined herein.
[0266] In accordance with the invention, the term "pharmaceutical
composition" relates to a composition for administration to a
patient, preferably a human patient. The particular preferred
pharmaceutical composition of this invention comprises bispecific
single chain antibodies directed against and generated against
context-independent CD3 epitopes. Preferably, the pharmaceutical
composition comprises suitable formulations of carriers,
stabilizers and/or excipients. In a preferred embodiment, the
pharmaceutical composition comprises a composition for parenteral,
transdermal, intraluminal, intraarterial, intrathecal and/or
intranasal administration or by direct injection into tissue. It is
in particular envisaged that said composition is administered to a
patient via infusion or injection. Administration of the suitable
compositions may be effected by different ways, e.g., by
intravenous, intraperitoneal, subcutaneous, intramuscular, topical
or intradermal administration. In particular, the present invention
provides for an uninterrupted administration of the suitable
composition. As a non-limiting example, uninterrupted, i.e.
continuous administration may be realized by a small pump system
worn by the patient for metering the influx of therapeutic agent
into the body of the patient. The pharmaceutical composition
comprising the bispecific single chain antibodies directed against
and generated against context-independent CD3 epitopes of the
invention can be administered by using said pump systems. Such pump
systems are generally known in the art, and commonly rely on
periodic exchange of cartridges containing the therapeutic agent to
be infused. When exchanging the cartridge in such a pump system, a
temporary interruption of the otherwise uninterrupted flow of
therapeutic agent into the body of the patient may ensue. In such a
case, the phase of administration prior to cartridge replacement
and the phase of administration following cartridge replacement
would still be considered within the meaning of the pharmaceutical
means and methods of the invention together make up one
"uninterrupted administration" of such therapeutic agent.
[0267] The continuous or uninterrupted administration of these
bispecific single chain antibodies directed against and generated
against context-independent CD3 epitopes of this invention may be
intravenuous or subcutaneous by way of a fluid delivery device or
small pump system including a fluid driving mechanism for driving
fluid out of a reservoir and an actuating mechanism for actuating
the driving mechanism. Pump systems for subcutaneous administration
may include a needle or a cannula for penetrating the skin of a
patient and delivering the suitable composition into the patient's
body. Said pump systems may be directly fixed or attached to the
skin of the patient independently of a vein, artery or blood
vessel, thereby allowing a direct contact between the pump system
and the skin of the patient. The pump system can be attached to the
skin of the patient for 24 hours up to several days. The pump
system may be of small size with a reservoir for small volumes. As
a non-limiting example, the volume of the reservoir for the
suitable pharmaceutical composition to be administered can be
between 0.1 and 50 ml.
[0268] The continuous administration may be transdermal by way of a
patch worn on the skin and replaced at intervals. One of skill in
the art is aware of patch systems for drug delivery suitable for
this purpose. It is of note that transdermal administration is
especially amenable to uninterrupted administration, as exchange of
a first exhausted patch can advantageously be accomplished
simultaneously with the placement of a new, second patch, for
example on the surface of the skin immediately adjacent to the
first exhausted patch and immediately prior to removal of the first
exhausted patch. Issues of flow interruption or power cell failure
do not arise.
[0269] The composition of the present invention, comprising in
particular bispecific single chain antibodies preferably directed
against and generated against context-independent CD3 epitopes may
further comprise a pharmaceutically acceptable carrier. Examples of
suitable pharmaceutical carriers are well known in the art and
include solutions, e.g. phosphate buffered saline solutions, water,
emulsions, such as oil/water emulsions, various types of wetting
agents, sterile solutions, liposomes, etc. Compositions comprising
such carriers can be formulated by well known conventional methods.
Formulations can comprise carbohydrates, buffer solutions, amino
acids and/or surfactants. Carbohydrates may be non-reducing sugars,
preferably trehalose, sucrose, octasulfate, sorbitol or xylitol.
Such formulations may be used for continuous administrations which
may be intravenuous or subcutaneous with and/or without pump
systems. Amino acids may be charged amino acids, preferably lysine,
lysine acetate, arginine, glutamate and/or histidine. Surfactants
may be detergents, preferably with a molecular weight of >1.2 KD
and/or a polyether, preferably with a molecular weight of >3 KD.
Non-limiting examples for preferred detergents are Tween 20, Tween
40, Tween 60, Tween 80 or Tween 85. Non-limiting examples for
preferred polyethers are PEG 3000, PEG 3350, PEG 4000 or PEG 5000.
Buffer systems used in the present invention can have a preferred
pH of 5-9 and may comprise citrate, succinate, phosphate, histidine
and acetate. The compositions of the present invention can be
administered to the subject at a suitable dose which can be
determined e.g. by dose escalating studies by administration of
increasing doses of the bispecific single chain antibody molecule
of the invention exhibiting cross-species specificity described
herein to non-chimpanzee primates, for instance macaques. As set
forth above, the bispecific single chain antibody molecule of the
invention exhibiting cross-species specificity described herein can
be advantageously used in identical form in preclinical testing in
non-chimpanzee primates and as drug in humans. These compositions
can also be administered in combination with other proteinaceous
and non-proteinaceous drugs. These drugs may be administered
simultaneously with the composition comprising the bispecific
single chain antibody molecule of the invention as defined herein
or separately before or after administration of said polypeptide in
timely defined intervals and doses. The dosage regimen will be
determined by the attending physician and clinical factors. As is
well known in the medical arts, dosages for any one patient depend
upon many factors, including the patient's size, body surface area,
age, the particular compound to be administered, sex, time and
route of administration, general health, and other drugs being
administered concurrently. Preparations for parenteral
administration include sterile aqueous or non-aqueous solutions,
suspensions, and emulsions. Examples of non-aqueous solvents are
propylene glycol, polyethylene glycol, vegetable oils such as olive
oil, and injectable organic esters such as ethyl oleate. Aqueous
carriers include water, alcoholic/aqueous solutions, emulsions or
suspensions, including saline and buffered media. Parenteral
vehicles include sodium chloride solution, Ringer's dextrose,
dextrose and sodium chloride, lactated Ringer's, or fixed oils.
Intravenous vehicles include fluid and nutrient replenishers,
electrolyte replenishers (such as those based on Ringer's
dextrose), and the like. Preservatives and other additives may also
be present such as, for example, antimicrobials, anti-oxidants,
chelating agents, inert gases and the like. In addition, the
composition of the present invention might comprise proteinaceous
carriers, like, e.g., serum albumin or immunoglobulin, preferably
of human origin. It is envisaged that the composition of the
invention might comprise, in addition to the bispecific single
chain antibody molecule of the invention defined herein, further
biologically active agents, depending on the intended use of the
composition. Such agents might be drugs acting on the
gastro-intestinal system, drugs acting as cytostatica, drugs
preventing hyperurikemia, drugs inhibiting immunoreactions (e.g.
corticosteroids), drugs modulating the inflammatory response, drugs
acting on the circulatory system and/or agents such as cytokines
known in the art.
[0270] The biological activity of the pharmaceutical composition
defined herein can be determined for instance by cytotoxicity
assays, as described in the following examples, in WO 99/54440 or
by Schlereth et al. (Cancer Immunol. Immunother. 20 (2005), 1-12).
"Efficacy" or "in vivo efficacy" as used herein refers to the
response to therapy by the pharmaceutical composition of the
invention, using e.g. standardized NCI response criteria. The
success or in vivo efficacy of the therapy using a pharmaceutical
composition of the invention refers to the effectiveness of the
composition for its intended purpose, i.e. the ability of the
composition to cause its desired effect, i.e. depletion of
pathologic cells, e.g. tumor cells. The in vivo efficacy may be
monitored by established standard methods for the respective
disease entities including, but not limited to white blood cell
counts, differentials, Fluorescence Activated Cell Sorting, bone
marrow aspiration. In addition, various disease specific clinical
chemistry parameters and other established standard methods may be
used. Furthermore, computer-aided tomography, X-ray, nuclear
magnetic resonance tomography (e.g. for National Cancer
Institute-criteria based response assessment [Cheson B D, Horning S
J, Coiffier B, Shipp M A, Fisher R I, Connors J M, Lister T A, Vose
J, Grillo-Lopez A, Hagenbeek A, Cabanillas F, Klippensten D,
Hiddemann W, Castellino R, Harris N L, Armitage J O, Carter W,
Hoppe R, Canellos G P. Report of an international workshop to
standardize response criteria for non-Hodgkin's lymphomas. NCI
Sponsored International Working Group. J Clin Oncol. 1999 April;
17(4):1244]), positron-emission tomography scanning, white blood
cell counts, differentials, Fluorescence Activated Cell Sorting,
bone marrow aspiration, lymph node biopsies/histologies, and
various cancer specific clinical chemistry parameters (e.g. lactate
dehydrogenase) and other established standard methods may be
used.
[0271] Another major challenge in the development of drugs such as
the pharmaceutical composition of the invention is the predictable
modulation of pharmacokinetic properties. To this end, a
pharmacokinetic profile of the drug candidate, i.e. a profile of
the pharmacokinetic parameters that effect the ability of a
particular drug to treat a given condition, is established.
Pharmacokinetic parameters of the drug influencing the ability of a
drug for treating a certain disease entity include, but are not
limited to: half-life, volume of distribution, hepatic first-pass
metabolism and the degree of blood serum binding. The efficacy of a
given drug agent can be influenced by each of the parameters
mentioned above.
[0272] "Half-life" means the time where 50% of an administered drug
are eliminated through biological processes, e.g. metabolism,
excretion, etc.
[0273] By "hepatic first-pass metabolism" is meant the propensity
of a drug to be metabolized upon first contact with the liver, i.e.
during its first pass through the liver.
[0274] "Volume of distribution" means the degree of retention of a
drug throughout the various compartments of the body, like e.g.
intracellular and extracellular spaces, tissues and organs, etc.
and the distribution of the drug within these compartments.
[0275] "Degree of blood serum binding" means the propensity of a
drug to interact with and bind to blood serum proteins, such as
albumin, leading to a reduction or loss of biological activity of
the drug.
[0276] Pharmacokinetic parameters also include bioavailability, lag
time (Tlag), Tmax, absorption rates, more onset and/or Cmax for a
given amount of drug administered.
[0277] "Bioavailability" means the amount of a drug in the blood
compartment.
[0278] "Lag time" means the time delay between the administration
of the drug and its detection and measurability in blood or
plasma.
[0279] "Tmax" is the time after which maximal blood concentration
of the drug is reached, and "Cmax" is the blood concentration
maximally obtained with a given drug. The time to reach a blood or
tissue concentration of the drug which is required for its
biological effect is influenced by all parameters. Pharmacokinetik
parameters of bispecific single chain antibodies exhibiting
cross-species specificity, which may be determined in preclinical
animal testing in non-chimpanzee primates as outlined above are
also set forth e.g. in the publication by Schlereth et al. (Cancer
Immunol. Immunother. 20 (2005), 1-12).
[0280] The term "toxicity" as used herein refers to the toxic
effects of a drug manifested in adverse events or severe adverse
events. These side events might refer to a lack of tolerability of
the drug in general and/or a lack of local tolerance after
administration. Toxicity could also include teratogenic or
carcinogenic effects caused by the drug.
[0281] The term "safety", "in vivo safety" or "tolerability" as
used herein defines the administration of a drug without inducing
severe adverse events directly after administration (local
tolerance) and during a longer period of application of the drug.
"Safety", "in vivo safety" or "tolerability" can be evaluated e.g.
at regular intervals during the treatment and follow-up period.
Measurements include clinical evaluation, e.g. organ
manifestations, and screening of laboratory abnormalities. Clinical
evaluation may be carried out and deviating to normal findings
recorded/coded according to NCI-CTC and/or MedDRA standards. Organ
manifestations may include criteria such as allergy/immunology,
blood/bone marrow, cardiac arrhythmia, coagulation and the like, as
set forth e.g. in the Common Terminology Criteria for adverse
events v3.0 (CTCAE). Laboratory parameters which may be tested
include for instance haematology, clinical chemistry, coagulation
profile and urine analysis and examination of other body fluids
such as serum, plasma, lymphoid or spinal fluid, liquor and the
like. Safety can thus be assessed e.g. by physical examination,
imaging techniques (i.e. ultrasound, x-ray, CT scans, Magnetic
Resonance Imaging (MRI), other measures with technical devices
(i.e. electrocardiogram), vital signs, by measuring laboratory
parameters and recording adverse events. For example, adverse
events in non-chimpanzee primates in the uses and methods according
to the invention may be examined by histopathological and/or
histochemical methods.
[0282] The term "effective and non-toxic dose" as used herein
refers to a tolerable dose of the bispecific single chain antibody
as defined herein which is high enough to cause depletion of
pathologic cells, tumor elimination, tumor shrinkage or
stabilization of disease without or essentially without major toxic
effects. Such effective and non-toxic doses may be determined e.g.
by dose escalation studies described in the art and should be below
the dose inducing severe adverse side events (dose limiting
toxicity, DLT).
[0283] The above terms are also referred to e.g. in the Preclinical
safety evaluation of biotechnology-derived pharmaceuticals S6; ICH
Harmonised Tripartite Guideline; ICH Steering Committee meeting on
Jul. 16, 1997.
[0284] Moreover, the invention relates to a pharmaceutical
composition comprising a bispecific single chain antibody molecule
of this invention or produced according to the process according to
the invention for the prevention, treatment or amelioration of
cancer or an autoimmune disease. Preferably, said cancer is a:
[0285] (a) a solid tumor, more preferably a carcinoma or prostate
cancer; [0286] (b) a carcinoma, sarcoma, glioblastoma/astrocytoma,
melanoma, mesothelioma, Wilms tumor or a hematopoietic malignancy
such as leukemia, lymphoma or multiple myeloma; [0287] (c)
carcinomas (breast, kidney, lung, colorectal, colon, pancreas
mesothelioma), sarcomas, and neuroectodermal tumors (melanoma,
glioma, neuroblastoma); [0288] (d) epithelial cancer; or [0289] (e)
bone or soft tissue cancer (e.g. Ewing sarcoma), breast, liver,
lung, head and neck, colorectal, prostate, leiomyosarcoma, cervical
and endometrial cancer, ovarian, prostate, and pancreatic
cancer.
[0290] Preferably, said pharmaceutical composition further
comprises suitable formulations of carriers, stabilizers and/or
excipients.
[0291] A further aspect of the invention relates to a use of a
bispecific single chain antibody molecule/polypeptide as defined
herein above or produced according to a process defined herein
above, for the preparation of a pharmaceutical composition for the
prevention, treatment or amelioration of a disease. Preferably,
said disease is cancer. More preferably, said cancer is a solid
tumor, preferably a carcinoma or prostate cancer.
[0292] In another preferred embodiment of use of the bispecific
single chain antibody molecule of the invention said pharmaceutical
composition is suitable to be administered in combination with an
additional drug, i.e. as part of a co-therapy. In said co-therapy,
an active agent may be optionally included in the same
pharmaceutical composition as the bispecific single chain antibody
molecule of the invention, or may be included in a separate
pharmaceutical composition. In this latter case, said separate
pharmaceutical composition is suitable for administration prior to,
simultaneously as or following administration of said
pharmaceutical composition comprising the bispecific single chain
antibody molecule of the invention. The additional drug or
pharmaceutical composition may be a non-proteinaceous compound or a
proteinaceous compound. In the case that the additional drug is a
proteinaceous compound, it is advantageous that the proteinaceous
compound be capable of providing an activation signal for immune
effector cells.
[0293] Preferably, said proteinaceous compound or non-proteinaceous
compound may be administered simultaneously or non-simultaneously
with the bispecific single chain antibody molecule of the
invention, a nucleic acid molecule as defined hereinabove, a vector
as defined as defined hereinabove, or a host as defined as defined
hereinabove.
[0294] Another aspect of the invention relates to a method for the
prevention, treatment or amelioration of a disease in a subject in
the need thereof, said method comprising the step of administration
of an effective amount of a pharmaceutical composition of the
invention. Preferably, said disease is cancer or an autoimmune
disease. Preferably, said cancer is [0295] (a) a solid tumor, more
preferably a carcinoma or prostate cancer; [0296] (b) a carcinoma,
sarcoma, glioblastoma/astrocytoma, melanoma, mesothelioma, Wilms
tumor or a hematopoietic malignancy such as leukemia, lymphoma or
multiple myeloma; [0297] (c) carcinomas (breast, kidney, lung,
colorectal, colon, pancreas mesothelioma), sarcomas, and
neuroectodermal tumors (melanoma, glioma, neuroblastoma); [0298]
(d) epithelial cancer; or [0299] (e) bone or soft tissue cancer
(e.g. Ewing sarcoma), breast, liver, lung, head and neck,
colorectal, prostate, leiomyosarcoma, cervical and endometrial
cancer, ovarian, prostate, and pancreatic cancer.
[0300] In another preferred embodiment of the method of the
invention said pharmaceutical composition is suitable to be
administered in combination with an additional drug, i.e. as part
of a co-therapy. In said co-therapy, an active agent may be
optionally included in the same pharmaceutical composition as the
bispecific single chain antibody molecule of the invention, or may
be included in a separate pharmaceutical composition. In this
latter case, said separate pharmaceutical composition is suitable
for administration prior to, simultaneously as or following
administration of said pharmaceutical composition comprising the
bispecific single chain antibody molecule of the invention. The
additional drug or pharmaceutical composition may be a
non-proteinaceous compound or a proteinaceous compound. In the case
that the additional drug is a proteinaceous compound, it is
advantageous that the proteinaceous compound be capable of
providing an activation signal for immune effector cells.
[0301] Preferably, said proteinaceous compound or non-proteinaceous
compound may be administered simultaneously or non-simultaneously
with the bispecific single chain antibody molecule of the
invention, a nucleic acid molecule as defined hereinabove, a vector
as defined as defined hereinabove, or a host as defined as defined
hereinabove.
[0302] It is preferred for the above described method of the
invention that said subject is a human.
[0303] In a further aspect, the invention relates to a kit
comprising a bispecific single chain antibody molecule of the
invention, a nucleic acid molecule of the invention, a vector of
the invention, or a host of the invention.
[0304] These and other embodiments are disclosed and encompassed by
the description and Examples of the present invention. Recombinant
techniques and methods in immunology are described e.g. in Sambrook
et al. Molecular Cloning: A Laboratory Manual; Cold Spring Harbor
Laboratory Press, 3.sup.rd edition 2001; Lefkovits; Immunology
Methods Manual; The Comprehensive Sourcebook of Techniques;
Academic Press, 1997; Golemis; Protein-Protein Interactions: A
Molecular Cloning Manual; Cold Spring Laboratory Press, 2002.
Further literature concerning any one of the antibodies, methods,
uses and compounds to be employed in accordance with the present
invention may be retrieved from public libraries and databases,
using for example electronic devices. For example, the public
database "Medline", available on the Internet, may be utilized, for
example under http://www.ncbi.nlm.nih.gov/PubMed/medline.html.
Further databases and addresses such as
http://www.ncbi.nlm.nih.gov/or listed at the EMBL-services homepage
under http://www.embl.de/services/index.html are known to the
person skilled in the art and can also be obtained using, e. g.,
http://www.google.com.
[0305] The figures show:
[0306] FIG. 1
[0307] Flowcytometry of CHO cells transfected with native human
EpCAM (positive control) and different EpCAM-hNG2 fusion proteins,
respectively. Staining with the murine parental IgG1 antibody MAb
5-10 (bold lines) directed against human EpCAM was performed as
described (Brischwein (2007) J Immunother 30: 798-807). PBS/2% FCS
instead of MAb 5-10 was used as negative control (thin lines).
[0308] FIG. 2
[0309] T cell cytotoxicity redirected by bscAb 5-10.times.I2C
against CHO cells transfected with human EpCAM (positive control)
and different EpCAM-hNG2 fusion proteins as measured in a chromium
51 (.sup.51Cr) release assay (y-axis). Stimulated human CD4/CD56
depleted PBMC served as effector T cells. Effector- to target cell
ratio was 10:1. BscAb 5-10.times.I2C was used as culture
supernatant at different dilutions as indicated on the x-axis.
Assay duration was 18 hours.
[0310] FIG. 3
[0311] Amino acid sequence alignment of full-length mature human
and rat PSMA. Mismatching homologous amino acid positions are
underlined and highlighted by bold character style. Numbering of
amino acid positions refers to human PSMA and starts with the amino
acid methionine encoded by the start codon of human PSMA.
Intracellular domain aa 1-aa 19; transmembrane domain aa 20-aa 43;
extracellular domain aa 44-aa 750.
[0312] FIG. 4
[0313] FACS binding analysis of I2C-based anti-human PSMA-bscAbs on
CHO cells transfected with (unmutated) human PSMA, rat PSMA mutated
to the homologous human amino acid at every mismatched amino acid
position with a membrane-distance of .gtoreq.60 .ANG., and
unmutated rat PSMA. The bold lines show staining by cell culture
supernatant of CHO cells transfected with PSMA-directed bispecific
antibody constructs. Cell culture supernatant of untransfected CHO
cells served as negative control (thin lines). PSMA-directed bscAbs
P1.times.I2C, P2.times.I2C, P3.times.I2C, P4.times.I2C and
P5.times.I2C bind to (unmutated) human PSMA but neither to
unmutated nor to mutated rat PSMA and thus confirms a
membrane-distance of <60 .ANG. for the PSMA-epitope of each of
these bispecific constructs. By contrast, PSMA-directed bscAbs
D1.times.I2C and D2.times.I2C do not bind to unmutated rat PSMA but
to (unmutated) human and mutated rat PSMA consistent with
PSMA-epitopes of a membrane-distance .gtoreq.60 .ANG..
[0314] FIG. 5
[0315] T cell cytotoxicity redirected by I2C-based PSMA-directed
bscAbs to CHO cells transfected with human PSMA as measured in a
chromium 51 (.sup.51Cr) release assay. As source of effector T
cells stimulated human CD4/CD56 depleted PBMC were used. The
effector-to-target cell ratio was 10:1. PSMA-directed bscAbs were
used as cell culture supernatants from transfected CHO cells at
different dilutions as indicated. The assay duration was 18 hours.
PSMA-directed bscAbs P1.times.I2C, P2.times.I2C, P3.times.I2C,
P4.times.I2C and P5.times.I2C, whose PSMA-epitopes have a
membrane-distance of <60 .ANG. are substantially more potent in
redirecting T cell cytotoxicity than PSMA-directed bscAbs
D1.times.I2C and D2.times.I2C, whose PSMA-epitopes have a
membrane-distance of .gtoreq.60 .ANG..
[0316] FIG. 6
[0317] FACS binding analysis of I2C-based anti-human PSMA-bscAbs on
CHO cells transfected with (unmutated) human PSMA, rat PSMA mutated
to the homologous human amino acid at every mismatched amino acid
position with a membrane-distance of .gtoreq.60 .ANG., and
unmutated rat PSMA. The bold lines show staining by cell culture
supernatant of CHO cells transfected with PSMA-directed bispecific
antibody constructs. Cell culture supernatant of untransfected CHO
cells served as negative control (thin lines). The PSMA-directed
bscAb P6.times.I2C binds to (unmutated) human PSMA but neither to
unmutated nor to mutated rat PSMA and thus confirms a
membrane-distance of <60 .ANG. for the PSMA-epitope of this
bispecific construct. By contrast, PSMA-directed bscAb D3.times.I2C
does not bind to unmutated rat PSMA but to (unmutated) human and
mutated rat PSMA consistent with a PSMA-epitope of a
membrane-distance .gtoreq.60 .ANG..
[0318] FIG. 7
[0319] T cell cytotoxicity redirected by I2C-based PSMA-directed
bscAbs to CHO cells transfected with human PSMA as measured in a
chromium 51 (.sup.51Cr) release assay. As source of effector T
cells stimulated human CD4/CD56 depleted PBMC were used. The
effector-to-target cell ratio was 10:1. PSMA-directed bscAbs were
used as cell culture supernatants from transfected CHO cells at
different dilutions as indicated. The assay duration was 18 hours.
PSMA-directed bscAb P6.times.I2C, whose PSMA-epitope has a
membrane-distance of <60 .ANG. is substantially more potent in
redirecting T cell cytotoxicity than PSMA-directed bscAb
D3.times.I2C, whose PSMA-epitope has a membrane-distance of
.gtoreq.60 .ANG..
[0320] FIG. 8
[0321] FACS binding analysis of I2C-based bscAbs directed to
membrane-proximal PSMA-epitopes on CHO cells transfected with
macaque PSMA, the CD3 positive human T cell leukemia cell line
HPB-ALL and the CD3 positive macaque T cell line 4119LnPx. The bold
lines show staining by cell culture supernatant of CHO cells
transfected with designated PSMA-directed bispecific antibody
constructs. Cell culture supernatant of untransfected CHO cells
served as negative control (thin lines). The designated
PSMA-directed bscAbs in addition to human PSMA also bind to macaque
PSMA, human CD3 and macaque CD3.
[0322] FIG. 9
[0323] Amino acid sequence alignment of full-length mature human
and murine FAP.alpha.. Mismatching homologous amino acid positions
are underlined and highlighted by bold character style. Numbering
of amino acid positions refers to human FAPalpha and starts with
the amino acid methionine encoded by the start codon of human
FAPalpha. Intracellular domain aa 1-aa 9; transmembrane domain aa
10-aa 26; extracellular domain aa 27-aa 760.
[0324] FIG. 10
[0325] FACS binding analysis of cell surface expression on CHO
cells expressing the murine FAPalpha antigen as described in
Example 6.3 and CHO cells expressing the mutated human FAPalpha
antigen with murine membrane-distal epitopes as described in
Example 6.4, respectively. The FACS staining was performed as
described in Examples 6.3 and 6.4. The bold lines represent cells
incubated with the detection antibodies--the Penta His antibody in
case of murine FAPalpha and the anti-FLAG M2 antibody in case of
the mutated human FAPalpha antigen with murine membrane-distal
epitopes. The thin lines represent the negative controls. For both
cell lines the overlay of the histograms for the anti-FLAG M2
antibody and the Penta His antibody, respectively, shows a
significant expression level of the respective antigen. Expression
levels were comparable for the two cell lines.
[0326] FIGS. 11A-11B
[0327] FACS binding analysis of designated bispecific single chain
constructs to CHO cells expressing human FAPalpha as described in
Example 6.1, the human CD3+ T cell line HPB-ALL, CHO cells
expressing macaque FAPalpha as described in Example 6.15 and the
macaque T cell line 4119LnPx, respectively. The FACS staining was
performed as described in Examples 6.13 and 6.16. The bold lines
represent cells incubated with cell culture supernatant of
transfected cells expressing the bispecific antibody constructs.
The thin lines represent the negative controls. Supernatant of
untransfected CHO cells was used as negative control. For each
bispecific single chain construct the overlays of the histograms
show specific binding of the construct to human and macaque
FAPalpha and human and macaque CD3.
[0328] FIGS. 12A-12C
[0329] The diagrams show results of chromium release assays
measuring cytotoxic activity induced by designated FAPalpha
specific single chain constructs redirected to the indicated target
cell lines generated as described in Examples 6.1, 6.3 and 6.4.
Effector cells were also used as indicated. The assays were
performed as described in Example 6.14. The diagrams clearly
demonstrate for each construct the potent recruitment of cytotoxic
activity of human effector T cells against target cells positive
for human FAPalpha and target cells positive for the mutated human
FAPalpha antigen with murine membrane-distal epitopes. No
significant recruitment of cytotoxic activity of human effector T
cells against target cells positive for murine FAPalpha was
detectable.
[0330] FIGS. 13A-13C
[0331] FACS binding analysis of designated bispecific single chain
constructs to CHO cells expressing human c-MET as described in
Example 7.17, the human CD3+ T cell line HPB-ALL, CHO cells
expressing macaque c-MET as described in Example 7.17 and the
macaque T cell line 4119LnPx, respectively. The FACS staining was
performed as described in Examples 7.13 and 7.16. The bold lines
represent cells incubated with cell culture supernatant of
transfected cells expressing the bispecific antibody constructs.
The filled histograms show the negative controls. Supernatant of
untransfected CHO cells was used as negative control. For each
bispecific single chain construct the overlays of the histograms
show specific binding of the construct to human and macaque c-MET
and human and macaque CD3.
[0332] FIGS. 14A-14D
[0333] FACS binding analysis of designated bispecific single chain
constructs to CHO cells expressing the murine c-MET antigen as
described in Example 7.17, CHO cells expressing the mutated human
c-MET antigen with murine membrane-distal epitopes as described in
Example 7.17 and CHO cells expressing the mutated murine c-MET
antigen with human membrane-distal epitopes as described in Example
7.17, respectively. The FACS staining was performed as described in
Example 7.13. The bold lines represent cells incubated with cell
culture supernatant of transfected cells expressing the bispecific
antibody constructs. The filled histograms show the negative
controls. Supernatant of untransfected CHO cells was used as
negative control. An anti-FLAG M2 antibody was used to detect
expression levels of the respective antigens. For each cell line
the overlay of the histograms for the anti-FLAG M2 antibody shows
high expression levels of the respective antigen. Expression levels
were comparable for the three cell lines. For each bispecific
single chain construct the overlays of the histograms show specific
binding of the construct to the mutated human c-MET antigen with
murine membrane-distal epitopes but not to the mutated murine c-MET
antigen with human membrane-distal epitopes and not to the murine
c-MET antigen.
[0334] FIGS. 15A-15C
[0335] The diagrams show results of chromium release assays
measuring cytotoxic activity induced by designated c-MET specific
single chain constructs redirected to the indicated target cell
lines generated as described in Example 7.17. Effector cells were
also used as indicated. The assays were performed as described in
Example 7.14. The diagrams clearly demonstrate for each construct
the potent recruitment of cytotoxic activity of human effector T
cells against target cells positive for human c-MET. No significant
recruitment of cytotoxic activity of human effector T cells against
target cells positive for murine c-MET and target cells positive
for the mutated murine c-MET antigen with human membrane-distal
epitopes, respectively, was detectable.
[0336] FIGS. 16A-16F
[0337] FACS binding analysis of designated cross-species specific
scFv antibodies to CHO cells expressing human c-MET as described in
Example 7.17, CHO cells expressing the murine c-MET antigen as
described in Example 7.17, CHO cells expressing the mutated human
c-MET antigen with murine membrane-distal epitopes as described in
Example 7.17 and CHO cells expressing the mutated murine c-MET
antigen with human membrane-distal epitopes as described in Example
7.17, respectively. The FACS staining was performed as described in
Example 7.9. The bold lines represent cells incubated with
periplasmic preparations containing the c-MET specific scFv
antibodies. The filled histograms show the negative controls. The
Buffer used for periplasmic preparations was used as negative
control. For each c-MET specific scFv antibody the overlays of the
histograms show specific binding of the construct to human c-MET
and human c-MET with murine membrane-distal epitopes. No
significant binding to cells positive for murine c-MET and to cells
positive for the mutated murine c-MET with human membrane-distal
epitopes, respectively, was detectable.
[0338] FIG. 17
[0339] FACS binding analysis of designated bispecific single chain
constructs to CHO cells expressing human IGF-1R as described in
Example 9.1, the human CD3+ T cell line HPB-ALL, CHO cells
expressing macaque IGF-1R as described in Example 9.15 and the
macaque T cell line 4119LnPx, respectively. The FACS staining was
performed as described in Examples 9.13 and 9.16. The bold lines
represent cells incubated with cell culture supernatant of
transfected cells expressing the bispecific antibody constructs.
The filled histograms show the negative controls. Supernatant of
untransfected CHO cells was used as negative control. For each
bispecific single chain construct the overlays of the histograms
show specific binding of the construct to human and macaque IGF-1R
and human and macaque CD3.
[0340] FIG. 18
[0341] FACS binding analysis of designated bispecific single chain
constructs to CHO cells expressing the murine IGF-1R antigen as
described in Example 9.3, CHO cells expressing the mutated human
IGF-1R antigen with murine membrane-distal epitopes as described in
Example 9.4 and CHO cells expressing the mutated murine IGF-1R
antigen with human membrane-distal epitopes as described in Example
9.5, respectively. The FACS staining was performed as described in
Example 9.13. The bold lines represent cells incubated with cell
culture supernatant of transfected cells expressing the bispecific
antibody constructs. The filled histograms show the negative
controls. Supernatant of untransfected CHO cells was used as
negative control. For each bispecific single chain construct the
overlays of the histograms show specific binding of the construct
to the mutated human IGF-1R antigen with murine membrane-distal
epitopes but not to the mutated murine IGF-1R antigen with human
membrane-distal epitopes and not to the murine IGF-1R antigen.
[0342] FIG. 19
[0343] The diagrams show results of chromium release assays
measuring cytotoxic activity induced by designated IGF-1R specific
single chain constructs redirected to the CHO cells expressing
human IGF-1R as described in Example 9.1. Effector cells were used
as indicated. The assays were performed as described in Example
9.14. The diagrams clearly demonstrate for each construct the
potent recruitment of cytotoxic activity of human effector T cells
against target cells positive for human IGF-1R.
[0344] FIGS. 20A-20B
[0345] FACS binding analysis of designated bispecific single chain
constructs to CHO cells expressing designated human/rat PSMA
chimeras as described in Example 10.2.1. The FACS staining was
performed as described in Example 10.2.2. The bold lines represent
cells incubated with cell culture supernatant of transfected cells
expressing the bispecific antibody constructs. The filled
histograms show the negative controls. Supernatant of untransfected
CHO cells was used as negative control. For each bispecific single
chain construct the overlays of the histograms show specific
binding of the construct to the chimeric constructs
huPSMArat140-169, huPSMArat281-284, huPSMArat300-344,
huPSMArat683-690 and huPSMArat716-750. Compared with the signals
obtained for the other bispecific single chain construct there is a
clear lack of binding for the bispecific single chain antibody
construct PSMA-P7 HL.times.I2C HL to the chimeric PSMA construct
huPSMArat598-617.
[0346] FIG. 21
[0347] The Figure shows binding signals obtained with periplasmic
preparations of the scFv antibody of the PSMA specific binder of
PSMA-D4 HL.times.I2C HL to 15-mer peptides spanning over the
extracellular domain of human PSMA and overlapping with their
neighboring peptides by 14 amino acids. Signals obtained for the
peptides are plotted on on the X-axis in order of the N-terminal
peptides on the left to the C-terminal peptides on the right.
Strength of ELISA signals using His detection is plotted on the
Y-axis. The ELISA was performed as described in Example 10.3. A
distinc maximum signal is detectable for the peptide spanning over
the amino acids threonine 334 to threonine 339.
[0348] FIG. 22
[0349] The diagram shows results of a CytoTox-Glo.TM. cytotoxicity
assay measuring cytotoxic activity of unstimulated human T cells
induced by designated PSMA specific bispecific single chain
constructs against CHO cells expressing human PSMA as described in
Example 2.1. The assay was performed as described in Example X.4.
The diagram clearly demonstrates the superior cytotoxic activity of
PSMA bispecific single chain antibody PSMA-P7 HL.times.I2C HL
directed at a membrane-proximal target epitope of human PSMA over
PSMA bispecific single chain antibody PSMA-D4 HL.times.I2C HL
directed at a membrane-distal target epitope of human PSMA.
TABLE LEGENDS
Table 1
[0350] All extracellular amino acids of human PSMA mismatching with
the homologous rat PSMA amino acid sequence. Those mismatched
extracellular human PSMA amino acids, whose alpha C-atoms have a
distance of .gtoreq.60 .ANG. from the alpha C-atom of the
thirteenth extracellular human PSMA amino acid (i.e. the reference
aa) as counted from the junction of transmembrane and extracellular
region are marked in bold. The distances between alpha C-atoms of
two amino acids within human PSMA were determined using the crystal
structure of human PSMA (accession No 1Z8L; obtained from the RCSB
pdb, protein data bank of the Research Collaboratory for Structural
Bioinformatics; http://www.rcsb.org/pdb) and the "measure distance
mode" of the software "3D molecule viewer" (a component of Vector
NTI Suite 8.0, Informax Inc.). Numbering of amino acid positions
refers to human PSMA and starts with the amino acid methionine
encoded by the start codon of human PSMA. The reference aa is
histidine at position 56.
Table 2
[0351] All extracellular amino acids of human FAPalpha mismatching
with the homologous murine FAPalpha amino acid sequence. Those
mismatched extracellular human FAPalpha amino acids, whose alpha
C-atoms have a distance of .gtoreq.60 .ANG. from the alpha C-atom
of the thirteenth extracellular human FAPalpha amino acid (i.e. the
reference aa) as counted from the junction of transmembrane and
extracellular region are marked in bold. The distances between
alpha C-atoms of two amino acids within human FAPalpha were
determined using the crystal structure of human FAPalpha (Accession
No 1Z68; obtained from the RCSB pdb, protein data bank of the
Research Collaboratory for Structural Bioinformatics;
http://www.rcsb.org/pdb) and the "measure distance mode" of the
software "3D molecule viewer" (a component of Vector NTI Suite 8.0,
Informax Inc.). Numbering of amino acid positions refers to human
FAPalpha and starts with the amino acid methionine encoded by the
start codon of human FAPalpha. The reference aa is methionine at
position 39.
[0352] The present invention is additionally described by way of
the following illustrative non-limiting examples that provide a
better understanding of the present invention and of its many
advantages.
EXAMPLES
[0353] 1. Cytotxicity with Respect to the Distance of the Target
Cell Epitopes Distance from the Target Cell Membrane
1.1. Generation of CHO Cells Expressing the Human EpCAM Antigen
[0354] The sequence of the human EpCAM antigen ('NM_002354, Homo
sapiens tumor-associated calcium signal transducer 1 (TACSTD1),
mRNA, National Center for Biotechnology Information,
http://www.ncbi.nlm.nih.gov/entrez) was used to obtain a synthetic
molecule by gene synthesis according to standard protocols. The
gene synthesis fragment was also designed as to contain a Kozak
site for eukaryotic expression of the construct and and restriction
sites at the beginning and the end of the DNA. The introduced
restriction sites XbaI at the 5' end and SalI at the 3' end were
utilised in the following cloning procedures. The gene synthesis
fragment was cloned via XbaI and SalI into a plasmid designated
pEF-DHFR (pEF-DHFR is described in Raum et al. Cancer Immunol
Immunother 50 (2001) 141-150). The aforementioned procedures were
carried out according to standard protocols (Sambrook, Molecular
Cloning; A Laboratory Manual, 3rd edition, Cold Spring Harbour
Laboratory Press, Cold Spring Harbour, New York (2001)). A clone
with sequence-verified nucleotide sequence was transfected into
DHFR deficient CHO cells for eukaryotic expression of the
construct. Eukaryotic protein expression in DHFR deficient CHO
cells was performed as described by Kaufmann R. J. (1990) Methods
Enzymol. 185, 537-566. Gene amplification of the construct was
induced by increasing concentrations of methotrexate (MTX) to a
final concentration of up to 20 nM MTX.
1.2. Generation of CHO Cells Expressing EpCAM-hNG2 Fusion
Proteins
[0355] The coding sequences of EpCAM-hNG2 fusion proteins
EpCAM-D1-hNG2 (SEQ ID Nos 189 and 190), EpCAM-D3-hNG2 (SEQ ID Nos
191 and 192), EpCAM-D1D3-hNG2 (SEQ ID Nos 193 and 194),
EpCAM-D1D2-hNG2 (SEQ ID Nos 195 and 196) and EpCAM-hNG2 (SEQ ID Nos
197 and 198) were obtained by gene synthesis according to standard
protocols. The gene synthesis fragment was designed as to contain
first the coding sequence of an immunoglobulin leader peptide
followed subsequently by human EpCAM, the respective extracellular
part of human NG2 and the transmembrane and cytoplasmic domain of
the human NG2 (Pluschke (1996) PNAS 93: 9710-9715). The different
components were connected by short peptide linkers. The gene
synthesis fragments were also designed as to introduce restriction
sites at the 5' end (Eco RI) and at the 3' end (Sal I) for cloning
into the mammalian cell expression vector pEF-DHFR (pEF-DHFR is
described in Raum et al. Cancer Immunol Immunother 50 (2001)
141-150). The aforementioned procedures were carried out according
to standard protocols (Sambrook, Molecular Cloning; A Laboratory
Manual, 3rd edition, Cold Spring Harbour Laboratory Press, Cold
Spring Harbour, New York (2001)). For each EpCAM-hNG2 fusion
protein .alpha. clone with sequence-verified nucleotide sequence
was transfected into DHFR deficient CHO cells for eukaryotic
expression. Eukaryotic protein expression in DHFR deficient CHO
cells was performed as described by Kaufmann R. J. (1990) Methods
Enzymol. 185, 537-566. Gene amplification of the construct was
induced by increasing concentrations of methotrexate (MTX) to a
final concentration of up to 20 nM MTX.
1.3. Generation of the EpCAM and CD3 Bispecific Single Antibody
5-10.times.I2C
[0356] The bispecific single chain antibody 5-10.times.I2C
comprising the scFv binding domain 5-10 (in VL-VH arrangement)
directed at human EpCAM (Brischwein (2007) J Immunother 30:
798-807) and the scFv binding domain I2C (in VL-VH arrangement)
directed at CD3epsilon on human T cells was obtained by gene
synthesis. The gene synthesis fragment was designed as to contain
first a Kozak site for eukaryotic expression of the construct,
followed by a 19 amino acid immunoglobulin leader peptide, followed
in frame by the coding sequence of the bispecific single chain
antibody 5-10.times.I2C, followed in frame by the coding sequence
of a 6 histidine tag and a stop codon (the cDNA and amino acid
sequence of the construct is listed under SEQ ID Nos 199 and 200).
The gene synthesis fragment was also designed as to introduce
suitable restriction sites at the beginning (EcoRI) and at the end
of the fragment (Sal I) for cloning of the gene synthesis fragment
into the mammalian cell expression vector pEF-DHFR (pEF-DHFR is
described in Raum et al. Cancer Immunol Immunother 50 (2001)
141-150). The aforementioned procedures were carried out according
to standard protocols (Sambrook, Molecular Cloning; A Laboratory
Manual, 3rd edition, Cold Spring Harbour Laboratory Press, Cold
Spring Harbour, New York (2001)). A clone with sequence-verified
nucleotide sequence was transfected into DHFR deficient CHO cells
for eukaryotic expression of the construct. Eukaryotic protein
expression in DHFR deficient CHO cells was performed as described
by Kaufmann R. J. (1990) Methods Enzymol. 185, 537-566. Gene
amplification of the construct was induced by increasing
concentrations of methotrexate (MTX) to a final concentration of up
to 20 nM MTX. After two passages of stationary culture cell culture
supernatant was collected and used in the subsequent
experiments.
1.4. Flowcytometry of CHO Cells Transfected with Different
EpCAM-hNG2 Fusion Proteins
[0357] The presence of the EpCAM-epitope of bispecific single chain
antibody 5-10.times.I2C on the CHO cells transfected with native
EpCAM and the EpCAM-hNG2 fusion proteins EpCAM-D1-hNG2,
EpCAM-D3-hNG2, EpCAM-D1 D3-hNG2, EpCAM-D1 D2-hNG2 and EpCAM-hNG2,
respectively, was confirmed by flowcytometry with the murine
parental IgG1 antibody Mab 5-10 as described (Brischwein (2007) J
Immunother 30: 798-807). The result is shown in FIG. 1.
1.5. T Cell Cytotoxicity Redirected by bscAb 5-10.times.I2C Against
CHO Cells Transfected with Different EpCAM-hNG2 Fusion Proteins
[0358] T cell cytotoxicity redirected by bscAb 5-10.times.I2C
against CHO cells transfected with different EpCAM-hNG2 fusion
proteins was measured in a chromium 51 (.sup.51Cr) release in vitro
cytotoxicity assay. As source of effector T cells stimulated human
CD4/CD56 depleted PBMC were used. Stimulated human PBMC were
obtained as follows: A Petri dish (145 mm diameter, Greiner bio-one
GmbH, Kremsmunster) was coated with a commercially available
anti-CD3 specific antibody (e.g. OKT3, Orthoclone) in a final
concentration of 1 .mu.g/ml for 1 hour at 37.degree. C. Unbound
protein was removed by one washing step with PBS. The fresh PBMC
were isolated from peripheral blood (30-50 ml human blood) by
Ficoll gradient centrifugation according to standard protocols.
3-5.times.10.sup.7 PBMC were added to the precoated petri dish in
120 ml of RPMI 1640 with stabilized glutamine/10% FCS/IL-2 20 U/ml
(Proleukin, Chiron) and stimulated for 2 days. On the third day the
cells were collected and washed once with RPMI 1640. IL-2 was added
to a final concentration of 20 U/ml and the cells were cultured
again for one day in the same cell culture medium as above.
[0359] By depletion of CD4+ T cells and CD56+NK cells according to
standard protocols CD8+ cytotoxic T lymphocytes (CTLs) were
enriched. Target cells were washed twice with PBS and labelled with
11.1 MBq .sup.51Cr in a final volume of 100 .mu.l RPMI with 50% FCS
for 60 minutes at 37.degree. C. Subsequently the labelled target
cells were washed 3 times with 5 ml RPMI and then used in the
cytotoxicity assay. The assay was performed in a 96 well plate in a
total volume of 250 .mu.l supplemented RPMI (as above) with an E:T
ratio of 10:1. BscAb 5-10.times.I2C was added as culture
supernatant from transfected CHO cells at different dilutions. The
assay time was 18 hours. Cytotoxicity was measured as relative
values of released chromium related to the difference of maximum
lysis (addition of Triton-X) and spontaneous lysis (without
effector cells). All measurements were carried out in
quadruplicates. Measurement of released chromium activity was
performed with a Wizard 3'' gammacounter (Perkin Elmer Life
Sciences GmbH, Koln, Germany). Analysis of the experimental data
was performed with Prism 4 for Windows (version 4.02, GraphPad
Software Inc., San Diego, Calif., USA). Sigmoidal dose response
curves typically had R.sup.2 values >0.90 as determined by the
software. As shown in FIG. 2 the T cell cytotoxicity redirected by
bscAb 5-10.times.I2C against the indicated target cells critically
depends on the varying distance of the target EpCAM epitope of bsc
5-10.times.I2C in the different EpCAM-hNG2 model antigens from the
target cell membrane. The descending order of T cell cytotoxicity
with increasing membrane distance of the target epitope as given in
parentheses is EpCAM-CHO (positive control)>EpCAM-D1-hNG2 (640
aa)>EpCAM-D3-hNG2 (679 aa)>EpCAM-D1 D3-hNG2 (871 aa). There
was no cytotoxic activity detectable against CHO cells expressing
EpCAM-D1 D2-hNG2 (1511 aa) or EpCAM-hNG2 (2190 aa).
2. Generation of Bispecific Single Chain Antibodies Directed at
Membrane-Proximal Target Epitopes of Human PSMA
2.1 Generation of CHO Cells Expressing Human PSMA
[0360] The coding sequence of human PSMA as published in GenBank
(Accession number NM_004476) is obtained by gene synthesis
according to standard protocols. The gene synthesis fragment is
designed as to contain first a Kozak site for eukaryotic expression
of the construct followed by the coding sequence of the human PSMA
protein and a stop codon (the cDNA and amino acid sequence of the
construct is listed under SEQ ID Nos 201 and 202). The gene
synthesis fragment is also designed as to introduce restriction
sites at the beginning and at the end of the fragment. The
introduced restriction sites, XbaI at the 5' end and SalI at the 3'
end, are utilized in the following cloning procedures. The gene
synthesis fragment is cloned via XbaI and SalI into a plasmid
designated pEF-DHFR (pEF-DHFR is described in Raum et al. Cancer
Immunol Immunother 50 (2001) 141-150) following standard protocols.
The aforementioned procedures are carried out according to standard
protocols (Sambrook, Molecular Cloning; A Laboratory Manual, 3rd
edition, Cold Spring Harbour Laboratory Press, Cold Spring Harbour,
New York (2001)). A clone with sequence-verified nucleotide
sequence is transfected into DHFR deficient CHO cells for
eukaryotic expression of the construct. Eukaryotic protein
expression in DHFR deficient CHO cells is performed as described by
Kaufmann R. J. (1990) Methods Enzymol. 185, 537-566. Gene
amplification of the construct is induced by increasing
concentrations of methotrexate (MTX) to a final concentration of up
to 20 nM MTX.
2.2 Generation of a Soluble Human PSMA Fusion Protein
[0361] The coding sequence of human PSMA as described in Example
2.1 and the coding sequence of murine Lag3 as published in GenBank
(Accession number NM_008479) are used for the construction of an
artificial cDNA sequence encoding a soluble fusion protein of human
PSMA and murine Lag3. To generate a construct for expression of the
soluble human PSMA fusion protein .alpha. cDNA fragment is obtained
by gene synthesis according to standard protocols (the cDNA and
amino acid sequence of the construct is listed under SEQ ID Nos 203
and 204). The gene synthesis fragment is designed as to contain
first a Kozak site for eukaryotic expression of the construct
followed by the coding sequence of the murine Lag3 protein from
amino acid 1 to 441 corresponding to the signal peptide and
extracellular domains of murine Lag3, followed in frame by the
coding sequence of an artificial
Ser.sub.1-Gly.sub.4-Ser.sub.1-linker, followed in frame by the
coding sequence of the human PSMA protein from amino acid 44 to 750
corresponding to the extracellular domains of human PSMA, followed
in frame by the coding sequence of an artificial
Ser.sub.1-Gly.sub.1-linker, followed in frame by the coding
sequence of a 6 histidine tag and a stop codon. The gene synthesis
fragment is also designed as to introduce restriction sites at the
beginning and at the end of the fragment. The introduced
restriction sites, XbaI at the 5' end and SalI at the 3' end, are
utilized in the following cloning procedures. The gene synthesis
fragment is cloned via XbaI and SalI into a plasmid designated
pEF-DHFR (pEF-DHFR is described in Raum et al. Cancer Immunol
Immunother 50 (2001) 141-150) following standard protocols. The
aforementioned procedures are all carried out according to standard
protocols (Sambrook, Molecular Cloning; A Laboratory Manual, 3rd
edition, Cold Spring Harbour Laboratory Press, Cold Spring Harbour,
New York (2001)). A clone with sequence-verified nucleotide
sequence is transfected into DHFR deficient CHO cells for
eukaryotic expression of the construct. Eukaryotic protein
expression in DHFR deficient CHO cells is performed as described by
Kaufmann R. J. (1990) Methods Enzymol. 185, 537-566. Gene
amplification of the construct is induced by increasing
concentrations of methotrexate (MTX) to a final concentration of up
to 20 nM MTX. After two passages of stationary culture the cells
are grown in roller bottles with nucleoside-free HyQ PF CHO liquid
soy medium (with 4.0 mM L-Glutamine with 0.1% Pluronic F--68;
HyClone) for 7 days before harvest. The cells are removed by
centrifugation and the supernatant containing the expressed protein
is stored at -20.degree. C. Alternatively a clone of the expression
plasmid with sequence-verified nucleotide sequence is used for
transfection and protein expression in the FreeStyle 293 Expression
System (Invitrogen GmbH, Karlsruhe, Germany) according to the
manufacturer's protocol. Supernatant containing the expressed
protein is obtained, cells are removed by centrifugation and the
supernatant is stored at -20.degree. C.
[0362] Purification of the soluble human PSMA fusion protein is
performed as follows: Akta.RTM. Explorer System (GE Health Systems)
and Unicorn.RTM. Software are used for chromatography. Immobilized
metal affinity chromatography ("IMAC") is performed using a
Fractogel EMD Chelate.RTM. (Merck) which is loaded with ZnCl.sub.2
according to the protocol provided by the manufacturer. The column
is equilibrated with buffer A (20 mM sodium phosphate buffer pH
7.2, 0.1 M NaCl) and the cell culture supernatant (500 ml) is
applied to the column (10 ml) at a flow rate of 3 ml/min. The
column is washed with buffer A to remove unbound sample. Bound
protein is eluted using a two step gradient of buffer B (20 mM
sodium phosphate buffer pH 7.2, 0.1 M NaCl, 0.5 M Imidazole)
according to the following procedure:
[0363] Step 1: 20% buffer B in 6 column volumes
[0364] Step 2: 100% buffer B in 6 column volumes
[0365] Eluted protein fractions from step 2 are pooled for further
purification. All chemicals are of research grade and purchased
from Sigma (Deisenhofen) or Merck (Darmstadt).
[0366] Gel filtration chromatography is performed on a HiLoad 16/60
Superdex 200 prep grade column (GE/Amersham) equilibrated with
Equi-buffer (25 mM Citrate, 200 mM Lysine, 5% Glycerol, pH 7.2).
Eluted protein samples (flow rate 1 ml/min) are subjected to
standard SDS-PAGE and Western Blot for detection. Prior to
purification, the column is calibrated for molecular weight
determination (molecular weight marker kit, Sigma MW GF-200).
Protein concentrations are determined using OD280 nm.
2.3 Generation of CHO Cells Expressing Rat PSMA
[0367] The sequence of rat PSMA (NM_057185, Rattus norvegicus
folate hydrolase (Folh1), mRNA, National Center for Biotechnology
Information, http://www.ncbi.nlm.nih.gov/entrez) is used to obtain
a synthetic cDNA molecule by gene synthesis according to standard
protocols. The gene synthesis fragment is designed as to contain
first a Kozak site for eukaryotic expression of the construct
followed by the complete coding sequence of the rat PSMA antigen,
followed in frame by the coding sequence of a FLAG-tag and a stop
codon (the cDNA and amino acid sequence of the construct is listed
under SEQ ID Nos 205 and 206). The gene synthesis fragment is also
designed as to introduce restriction sites at the 5' end (EcoRI)
and at the 3' end (SalI) of the cDNA fragment for cloning into the
mammalian cell expression vector pEF-DHFR (pEF-DHFR is described in
Raum et al. Cancer Immunol Immunother 50 (2001) 141-150). The
aforementioned procedures are carried out according to standard
protocols (Sambrook, Molecular Cloning; A Laboratory Manual, 3rd
edition, Cold Spring Harbour Laboratory Press, Cold Spring Harbour,
New York (2001)). A clone with sequence-verified nucleotide
sequence is transfected into DHFR deficient CHO cells for
eukaryotic expression of the construct.
[0368] Eukaryotic protein expression in DHFR deficient CHO cells is
performed as described by Kaufmann R. J. (1990) Methods Enzymol.
185, 537-566. Gene amplification for increased antigen expression
is induced by increasing concentrations of methotrexate (MTX) to a
final concentration of up to 20 nM MTX.
[0369] 2.4 Generation of CHO Cells Expressing a Mutated Human PSMA
Antigen with Rat Membrane-Distal Epitopes
[0370] The coding sequence of a mutated human PSMA antigen with rat
membrane-distal epitopes is obtained by gene synthesis according to
standard protocols The gene synthesis fragment is designed as to
contain first a Kozak site for eukaryotic expression of the
construct followed by the complete coding sequence of the human
PSMA antigen mutated at 12 specific amino acid positions as
explained below, followed in frame by the coding sequence of a FLAG
tag and a stop codon (the cDNA and amino acid sequence of the
construct is listed under SEQ ID Nos 207 and 208). All
extracellular amino acids of human PSMA mismatching with the
homologous rat sequence, whose alpha C-atoms have a distance of
.gtoreq.60 .ANG. from the alpha C-atom of the thirteenth
extracellular amino acid (i.e. the reference aa) as counted from
the junction of transmembrane and extracellular region, are mutated
to the homologous mismatched rat amino acid. This applies to the 12
amino acids that are listed in table Table 1 and marked in bold.
The homologous mismatched amino acids between human and rat PSMA
are identified by sequence alignment as shown in FIG. 3. The gene
synthesis fragment is also designed as to introduce restriction
sites at the 5' end (Xba I) and at the 3' end (Sal I) of the cDNA
fragment for cloning into the mammalian cell expression vector
pEF-DHFR (pEF-DHFR is described in Raum et al. Cancer Immunol
Immunother 50 (2001) 141-150). The aforementioned procedures are
carried out according to standard protocols (Sambrook, Molecular
Cloning; A Laboratory Manual, 3rd edition, Cold Spring Harbour
Laboratory Press, Cold Spring Harbour, New York (2001)). A clone
with sequence-verified nucleotide sequence is transfected into DHFR
deficient CHO cells for eukaryotic expression of the construct.
Eukaryotic protein expression in DHFR deficient CHO cells is
performed as described by Kaufmann R. J. (1990) Methods Enzymol.
185, 537-566. Gene amplification for increased antigen expression
is induced by increasing concentrations of methotrexate (MTX) to a
final concentration of up to 20 nM MTX.
[0371] 2.5 Generation of CHO Cells Expressing a Mutated Rat PSMA
Antigen with Human Membrane-Distal Epitopes
[0372] The coding sequence of a mutated rat PSMA antigen with human
membrane-distal epitopes is obtained by gene synthesis according to
standard protocols The gene synthesis fragment is designed as to
contain first a Kozak site for eukaryotic expression of the
construct followed by the complete coding sequence of the rat PSMA
antigen mutated at the same 12 specific extracellular amino acid
positions as identified in the foregoing Example 2.4 to the
respective homologous human amino acid, followed in frame by the
coding sequence of a FLAG tag and a stop codon (the cDNA and amino
acid sequence of the construct is listed under SEQ ID Nos 209 and
210). The gene synthesis fragment is also designed as to introduce
restriction sites at the 5' end (EcoRI I) and at the 3' end (Sal I)
of the cDNA fragment for cloning into the mammalian cell expression
vector pEF-DHFR (pEF-DHFR is described in Raum et al. Cancer
Immunol Immunother 50 (2001) 141-150). The aforementioned
procedures are carried out according to standard protocols
(Sambrook, Molecular Cloning; A Laboratory Manual, 3rd edition,
Cold Spring Harbour Laboratory Press, Cold Spring Harbour, New York
(2001)). A clone with sequence-verified nucleotide sequence is
transfected into DHFR deficient CHO cells for eukaryotic expression
of the construct. Eukaryotic protein expression in DHFR deficient
CHO cells is performed as described by Kaufmann R. J. (1990)
Methods Enzymol. 185, 537-566.
[0373] Gene amplification for increased antigen expression is
induced by increasing concentrations of methotrexate (MTX) to a
final concentration of up to 20 nM MTX.
[0374] 2.6 Immunization of mice using a soluble human PSMA fusion
protein Twelve weeks old F1 mice from BALB/c.times.C57BL/6
crossings are immunized with the soluble human PSMA fusion protein
as described in Example 2.2 To this end for each animal 40 .mu.g of
the soluble human PSMA fusion protein are mixed with 10 nmol of a
thioate-modified CpG-Oligonucleotide (5'-tccatgacgttcctgatgct-3')
in 300 .mu.l PBS and are injected intraperitoneally. Mice receive
booster immunizations after 21, 42 and optionally 63 days in the
same way. Ten days after the first booster immunization, blood
samples are taken and antibody serum titers against human PSMA are
tested by flow cytometry according to standard protocols. To this
end 200.000 cells of the human PSMA transfected CHO cells as
described in Example 2.1 are incubated for 30 min on ice with 50
.mu.l of serum of the immunized animals diluted 1:1000 in PBS with
2% FCS. The cells are washed twice in PBS with 2% FCS and binding
of serum antibodies is detected with an mouse Fc gamma-specific
antibody (Dianova) conjugated to phycoerythrin, diluted 1:100 in
PBS with 2% FCS. Serum of the animals obtained prior to
immunization is used as a negative control. Flow cytometry is
performed on a FACS-Calibur apparatus, the CellQuest software is
used to acquire and analyze the data (Becton Dickinson biosciences,
Heidelberg).
[0375] FACS staining and measuring of the fluorescence intensity
are performed as described in Current Protocols in Immunology
(Coligan, Kruisbeek, Margulies, Shevach and Strober,
Wiley-Interscience, 2002).
[0376] Animals demonstrating significant serum reactivity against
human PSMA as determined by the FACS analysis are used in the
subsequent experiment.
[0377] 2.7 Generation of an immune murine antibody scFv library:
Construction of a combinatorial antibody library and phage display
Three days after the last booster immunization spleen cells of
reactive animals are harvested for the preparation of total RNA
according to standard protocols. A library of murine immunoglobulin
(Ig) light chain (kappa) variable region (VK) and
[0378] Ig heavy chain variable region (VH) DNA-fragments is
constructed by RT-PCR on murine spleen RNA using VK- and VH
specific primers. cDNA is synthesized according to standard
protocols.
[0379] The primers are designed in a way to give rise to a 5'-XhoI
and a 3'-BstElI recognition site for the amplified heavy chain
V-fragments and to a 5'-SacI and a 3'-SpeI recognition site for
amplified VK DNA fragments.
[0380] For the PCR-amplification of the VH DNA-fragments eight
different 5'-VH-family specific primers (MVH1(GC)AG GTG CAG CTC GAG
GAG TCA GGA CCT SEQ ID NO: 211; MVH2 GAG GTC CAG CTC GAG CAG TCT
GGA CCT SEQ ID NO: 212; MVH3 CAG GTC CAA CTC GAG CAG CCT GGG GCT
SEQ ID NO: 213; MVH4 GAG GTT CAG CTC GAG CAG TCT GGG GCA SEQ ID NO:
214; MVH5 GA(AG) GTG AAG CTC GAG GAG TCT GGA GGA SEQ ID NO: 215;
MVH6 GAG GTG AAG CTT CTC GAG TCT GGA GGT SEQ ID NO: 216; MVH7 GAA
GTG AAG CTC GAG GAG TCT GGG GGA SEQ ID NO: 217; MVH8 GAG GTT CAG
CTC GAG CAG TCT GGA GCT SEQ ID NO: 218) are each combined with one
3'-VH primer (3'MuVHBstElI tga gga gac ggt gac cgt ggt ccc ttg gcc
cca g SEQ ID NO: 219); for the PCR amplification of the VK-chain
fragments seven different 5'-VK-family specific primers (MUVK1 CCA
GTT CCG AGC TCG TTG TGA CTC AGG AAT CT SEQ ID NO: 220; MUVK2 CCA
GTT CCG AGC TCG TGT TGA CGC AGC CGC CC SEQ ID NO: 221; MUVK3 CCA
GTT CCG AGC TCG TGC TCA CCC AGT CTC CA SEQ ID NO: 222; MUVK4 CCA
GTT CCG AGC TCC AGA TGA CCC AGT CTC CA SEQ ID NO: 223; MUVK5 CCA
GAT GTG AGC TCG TGA TGA CCC AGA CTC CA SEQ ID NO: 224; MUVK6 CCA
GAT GTG AGC TCG TCA TGA CCC AGT CTC CA SEQ ID NO: 225; MUVK7 CCA
GTT CCG AGC TCG TGA TGA CAC AGT CTC CA SEQ ID NO: 226) are each
combined with one 3'-VK primer (3'MuVkHindIII/BsiW1 tgg tgc act agt
cgt acg ttt gat ctc aag ctt ggt ccc SEQ ID NO: 227).
[0381] The following PCR program is used for amplification:
denaturation at 94.degree. C. for 20 sec; primer annealing at
52.degree. C. for 50 sec and primer extension at 72.degree. C. for
60 sec and 40 cycles, followed by a 10 min final extension at
72.degree. C.
[0382] 450 ng of the kappa light chain fragments (SacI-SpeI
digested) are ligated with 1400 ng of the phagemid pComb3H5Bhis
(SacI-SpeI digested; large fragment). The resulting combinatorial
antibody library is then transformed into 300 .mu.l of
electrocompetent Escherichia coli XL1 Blue cells by electroporation
(2.5 kV, 0.2 cm gap cuvette, 25 .mu.FD, 200 Ohm, Biorad
gene-pulser) resulting in a library size of more than 10.sup.7
independent clones. After one hour of phenotype expression,
positive transformants are selected for carbenicillin resistance
encoded by the pComb3H5BHis vector in 100 ml of liquid super broth
(SB)-culture over night. Cells are then harvested by centrifugation
and plasmid preparation is carried out using a commercially
available plasmid preparation kit (Qiagen).
[0383] 2800 ng of this plasmid-DNA containing the VK-library
(XhoI-BstElI digested; large fragment) are ligated with 900 ng of
the heavy chain V-fragments (XhoI-BstElI digested) and again
transformed into two 300 .mu.l aliquots of electrocompetent E. coli
XL1 Blue cells by electroporation (2.5 kV, 0.2 cm gap cuvette, 25
.mu.FD, 200 Ohm) resulting in a total VH-VK scFv (single chain
variable fragment) library size of more than 10.sup.7 independent
clones.
[0384] After phenotype expression and slow adaptation to
carbenicillin, the E. coli cells containing the antibody library
are transferred into SB-Carbenicillin (SB with 50 .mu.g/mL
carbenicillin) selection medium. The E. coli cells containing the
antibody library are then infected with an infectious dose of
10.sup.12 particles of helper phage VCSM13 resulting in the
production and secretion of filamentous M13 phage, wherein each
phage particle contains single stranded pComb3H5BHis-DNA encoding a
murine scFv-fragment and displays the corresponding scFv-protein as
a translational fusion to phage coat protein III. This pool of
phages displaying the antibody library is later used for the
selection of antigen binding entities.
[0385] 2.8 Phage Display Based Selection of Membrane-Proximal
Target Binders on CHO Cells Expressing the Mutated Human PSMA
Antigen with Rat Membrane-Distal Epitopes
[0386] The phage library carrying the cloned scFv-repertoire is
harvested from the respective culture supernatant by PEG8000/NaCl
precipitation and centrifugation. Approximately 10.sup.11 to
10.sup.12 scFv phage particles are resuspended in 0.4 ml of
PBS/0.1% BSA and incubated with 10.sup.5 to 10.sup.7 CHO cells
expressing the mutated human PSMA antigen with rat membrane-distal
epitopes as described in example 2.4 for 1 hour on ice under slow
agitation. These CHO cells are grown beforehand, harvested by
centrifugation, washed in PBS and resuspended in PBS/1% FCS
(containing Na Azide). scFv phage which do not specifically bind to
the CHO cells are eliminated by up to five washing steps with
PBS/1% FCS (containing Na Azide). After washing, binding entities
are eluted from the cells by resuspending the cells in HCl-glycine
pH 2.2 (10 min incubation with subsequent vortexing) and after
neutralization with 2 M Tris pH 12, the eluate is used for
infection of a fresh uninfected E. coli XL1 Blue culture
(OD600>0.5). The E. coli culture containing E. coli cells
successfully transduced with a phagemid copy, encoding a murine
scFv-fragment, are again selected for carbenicillin resistance and
subsequently infected with VCMS 13 helper phage to start the second
round of antibody display and in vitro selection. Typically a total
of 4 to 5 rounds of selections are carried out.
2.9 Screening for Membrane-Proximal Target Binders on CHO Cells
Expressing the Human PSMA Antigen, the Rat PSMA Antigen and the
Mutated Rat PSMA Antigen with Human Membrane-Distal Epitopes
[0387] Plasmid DNA corresponding to 4 and 5 rounds of panning is
isolated from E. coli cultures after selection. For the production
of soluble scFv-protein, VH-VL-DNA fragments are excised from the
plasmids (XhoI-SpeI). These fragments are cloned via the same
restriction sites in the plasmid pComb3H5BFlag/His differing from
the original pComb3H5BHis in that the expression construct (e.g.
scFv) includes a Flag-tag (TGDYKDDDDK) between the scFv and the
His6-tag and the additional phage proteins are deleted. After
ligation, each pool (different rounds of panning) of plasmid DNA is
transformed into 100 .mu.l heat shock competent E. coli TG1 or XLI
blue and plated onto carbenicillin LB-agar. Single colonies are
picked into 100 .mu.l of LB carb (LB with 50 .mu.g/ml
carbenicillin).
[0388] After induction with 1 mM IPTG E. coli transformed with
pComb3H5BFlag/His containing a VL- and VH-segment produce soluble
scFv in sufficient amounts. Due to a suitable signal sequence, the
scFv is exported into the periplasma where it folds into a
functional conformation.
[0389] Single E. coli bacterial colonies from the transformation
plates are picked for periplasmic small scale preparations and
grown in SB-medium (e.g. 10 ml) supplemented with 20 mM MgCl.sub.2
and carbenicillin 50 .mu.g/ml (and re-dissolved in PBS (e.g. 1 ml)
after harvesting. A temperature shock is applied by four rounds of
freezing at -70.degree. C. and thawing at 37.degree. C. whereby the
outer membrane of the bacteria is destroyed and the soluble
periplasmic proteins including the scFvs are released into the
supernatant. After elimination of intact cells and cell-debris by
centrifugation, the supernatant containing the murine anti-human
PSMA-scFvs is collected and used for further examination.
[0390] Screening of the isolated scFvs for membrane-proximal target
binders is performed by flow cytometry on CHO cells expressing the
human PSMA antigen as described in Example 2.1, the rat PSMA
antigen as described in Example 2.3 and the mutated rat PSMA
antigen with human membrane-distal epitopes as described in Example
2.5.
[0391] For flow cytometry 2.5.times.10.sup.5 cells of the
respective cell lines are incubated with 50 .mu.l supernatant. The
binding of the constructs is detected with an anti-His antibody
(Penta-His Antibody, BSA free, Qiagen GmbH, Hilden, FRG) at 2
.mu.g/ml in 50 .mu.l PBS with 2% FCS. As a second step reagent a
R-Phycoerythrin-conjugated affinity purified F(ab')2 fragment, goat
anti-mouse IgG (Fc-gamma fragment specific), diluted 1:100 in 50
.mu.l PBS with 2% FCS (Dianova, Hamburg, FRG) is used. The samples
are measured on a FACSscan (BD biosciences, Heidelberg, FRG).
[0392] Only constructs which show binding to CHO cells expressing
the human PSMA antigen and do not show binding to CHO cells
expressing the rat PSMA antigen and also do not show binding to CHO
cells expressing the mutated rat PSMA antigen with human
membrane-distal epitopes are selected for further use.
2.10 Generation of Human/Humanized Equivalents of Non-Human scFvs
to Membrane-Proximal Target Epitopes of Human PSMA
[0393] The VH region of a murine anti-PSMA scFv to a
membrane-proximal target epitope of human PSMA is aligned against
human antibody germline amino acid sequences.
[0394] The human antibody germline VH sequence is chosen which has
the closest homology to the non-human VH and a direct alignment of
the two amino acid sequences is performed. There are a number of
framework residues of the non-human VH that differ from the human
VH framework regions ("different framework positions"). Some of
these residues may contribute to the binding and activity of the
antibody to its target.
[0395] To construct a library that contains the murine CDRs and at
every framework position that differs from the chosen human VH
sequence both possible residues (the human and the maternal murine
amino acid residue), degenerated oligonucleotides are synthesized.
These oligonucleotides incorporate at the differing positions the
human residue with a probability of 75% and the murine residue with
a probability of 25%. For one human VH e.g. six of these
oligonucleotides have to be synthesized that overlap in a terminal
stretch of approximately 20 nucleotides. To this end every second
primer is an antisense primer. Restriction sites within the
oligonucleotides needed for later cloning are deleted.
[0396] These primers may have a length of 60 to 90 nucleotides,
depending on the number of primers that are needed to span over the
whole V sequence.
[0397] These e.g. six primers are mixed in equal amounts (e.g. 1
.mu.l of each primer (primer stocks 20 to 100 .mu.M) to a 20 .mu.l
PCR reaction) and added to a PCR mix consisting of PCR buffer,
nucleotides and Taq polymerase. This mix is incubated at 94.degree.
C. for 3 minutes, 65.degree. C. for 1 minute, 62.degree. C. for 1
minute, 59.degree. C. for 1 minute, 56.degree. C. for 1 minute,
52.degree. C. for 1 minute, 50.degree. C. for 1 minute and at
72.degree. C. for 10 minutes in a PCR cycler. Subsequently the
product is run in an agarose gel electrophoresis and the product of
a size from 200 to 400 base pairs isolated from the gel according
to standard methods.
[0398] This PCR product is then used as a template for a standard
PCR reaction using primers that incorporate suitable N-terminal and
C-terminal cloning restriction sites. The DNA fragment of the
correct size (for a VH approximately 350 nucleotides) is isolated
by agarose gel electrophoresis according to standard methods. In
this way sufficient VH DNA fragment is amplified. This VH fragment
is now a pool of VH fragments that have each one a different amount
of human and murine residues at the respective differing framework
positions (pool of humanized VH). The same procedure is performed
for the VL region of the murine anti-PSMA scFv to a
membrane-proximal target epitope of human PSMA (pool of humanized
VL).
[0399] The pool of humanized VH is then combined with the pool of
humanized VL in the phage display vector pComb3H5Bhis to form a
library of functional scFvs from which--after display on
filamentous phage--anti-PSMA binders to membrane-proximal target
epitopes of human PSMA are selected, screened, identified and
confirmed as described above for the parental non-human (murine)
anti-PSMA scFv. Single clones are then analyzed for favorable
properties and amino acid sequence. Those scFvs, which are closest
in amino acid sequence homology to human germline V-segments, are
preferred.
[0400] Human/humanized anti-PSMA scFvs to membrane-proximal target
epitopes of human PSMA are converted into recombinant bispecific
single chain antibodies and further characterized as follows.
2.11 Generation of I2C-Based Bispecific Single Chain Antibodies
Directed at Membrane-Proximal Target Epitopes of Human PSMA
[0401] Anti-PSMA scFvs to membrane-proximal target epitopes of
human PSMA with favorable properties and amino acid sequence are
converted into recombinant bispecific single chain antibodies by
joining them via a Gly.sub.4Ser.sub.1-linker with the CD3 specific
scFv I2C (SEQ ID NO: 185) to result in constructs with the domain
arrangement
VH.sub.PSMA-(Gly.sub.4Ser.sub.1).sub.3-VL.sub.PSMA-Ser.sub.1Gly.sub.4Ser.-
sub.1-VH.sub.CD3-(Gly.sub.4Ser.sub.1).sub.3-VL.sub.CD3.
Alternatively further constructs with different domain arrangements
can be generated according to standard protocolls. For expression
in CHO cells the coding sequences of (i) an N-terminal
immunoglobulin heavy chain leader comprising a start codon embedded
within a Kozak consensus sequence and (ii) a C-terminal His6-tag
followed by a stop codon are both attached in frame to the
nucleotide sequence encoding the bispecific single chain antibodies
prior to insertion of the resulting DNA-fragment as obtained by
gene synthesis into the multiple cloning site of the expression
vector pEF-DHFR (Raum et al. Cancer Immunol Immunother 50 (2001)
141-150). A clone with sequence-verified nucleotide sequence is
transfected into DHFR deficient CHO cells for eukaryotic expression
of the construct. Eukaryotic protein expression in DHFR deficient
CHO cells is performed as described by Kaufmann R. J. (1990)
Methods Enzymol. 185, 537-566. Gene amplification of the construct
is induced by increasing concentrations of methotrexate (MTX) to a
final concentration of up to 20 nM MTX.
2.12 Expression and Purification of Bispecific Single Chain
Antibody Molecules Directed at Membrane-Proximal Target Epitopes of
Human PSMA
[0402] Bispecific single chain antibody molecules are expressed in
Chinese hamster ovary cells (CHO). Eukaryotic protein expression in
DHFR deficient CHO cells is performed as described by Kaufmann R.
J. (1990) Methods Enzymol. 185, 537-566. Gene amplification of the
constructs is induced by addition of increasing concentrations of
MTX up to final concentrations of 20 nM MTX. After two passages of
stationary culture cell culture supernatant is collected and used
in the subsequent experiments. To generate supernatant for
purification after two passages of stationary culture the cells are
grown in roller bottles with nucleoside-free HyQ PF CHO liquid soy
medium (with 4.0 mM L-Glutamine with 0.1% Pluronic F-68; HyClone)
for 7 days before harvest. The cells are removed by centrifugation
and the supernatant containing the expressed protein is stored at
-20.degree. C. Alternatively, constructs are transiently expressed
in HEK 293 cells. Transfection is performed with 293fectin reagent
(Invitrogen, #12347-019) according to the manufacturer's protocol.
Furthermore the constructs are alternatively expressed in
transiently transfected DHFR deficient CHO cells using for example
FuGENE.RTM. HD Transfection Reagent (Roche Diagnostics GmbH, Cat.
No. 04709691001) according to the manufacturer's protocol.
[0403] Akta.RTM. Explorer System (GE Health Systems) and
Unicorn.RTM. Software are used for chromatography. Immobilized
metal affinity chromatography ("IMAC") is performed using a
Fractogel EMD Chelate.RTM. (Merck) which is loaded with ZnCl.sub.2
according to the protocol provided by the manufacturer. The column
is equilibrated with buffer A (20 mM sodium phosphate buffer pH
7.2, 0.1 M NaCl) and the cell culture supernatant (500 ml) is
applied to the column (10 ml) at a flow rate of 3 ml/min. The
column is washed with buffer A to remove unbound sample. Bound
protein is eluted using a two step gradient of buffer B (20 mM
sodium phosphate buffer pH 7.2, 0.1 M NaCl, 0.5 M Imidazole)
according to the following procedure:
[0404] Step 1: 20% buffer B in 6 column volumes
[0405] Step 2: 100% buffer B in 6 column volumes
[0406] Eluted protein fractions from step 2 are pooled for further
purification. All chemicals are of research grade and purchased
from Sigma (Deisenhofen) or Merck (Darmstadt).
[0407] Gel filtration chromatography is performed on a HiLoad 16/60
Superdex 200 prep grade column (GE/Amersham) equilibrated with
Equi-buffer (25 mM Citrate, 200 mM Lysine, 5% Glycerol, pH 7.2).
Eluted protein samples (flow rate 1 ml/min) are subjected to
standard SDS-PAGE and Western Blot for detection. Prior to
purification, the column is calibrated for molecular weight
determination (molecular weight marker kit, Sigma MW GF-200).
Protein concentrations are determined using OD280 nm.
[0408] Purified bispecific single chain antibody protein is
analyzed in SDS PAGE under reducing conditions performed with
pre-cast 4-12% Bis Tris gels (Invitrogen). Sample preparation and
application are performed according to the protocol provided by the
manufacturer. The molecular weight is determined with MultiMark
protein standard (Invitrogen). The gel is stained with colloidal
Coomassie (Invitrogen protocol). The purity of the isolated protein
is typically >95% as determined by SDS-PAGE.
[0409] The bispecific single chain antibody has a molecular weight
of about 52 kDa under native conditions as determined by gel
filtration in PBS.
[0410] Western Blot is performed using an Optitran.RTM. BA-S83
membrane and the Invitrogen Blot Module according to the protocol
provided by the manufacturer. The antibody used is directed against
the His Tag (Penta His, Qiagen) and a Goat-anti-mouse Ig labeled
with alkaline phosphatase (AP) (Sigma) is used as second step
reagent, and BCIP/NBT (Sigma) as substrate. A band detected at 52
kD corresponds to purified bispecific single chain antibodies.
2.13 Flow Cytometric Binding Analysis of Bispecific Antibodies
Directed at Membrane-Proximal Target Epitopes of Human PSMA
[0411] In order to test the functionality of bispecific antibody
constructs regarding the capability to bind to CD3 and to
membrane-proximal target epitopes of human PSMA, respectively, a
FACS analysis is performed. For this purpose CHO cells transfected
with human PSMA as described in Example 2.1 and the human CD3
positive T cell leukemia cell line HPB-ALL (DSMZ, Braunschweig,
ACC483) are used. For confirmation of binding to membrane-proximal
target epitopes of human PSMA--in addition--CHO cells expressing
the rat PSMA antigen as described in Example 2.3 and CHO cells
expressing the mutated rat PSMA antigen with human membrane-distal
epitopes as described in Example 2.5 are used. 200.000 cells of the
respective cell lines are incubated for 30 min on ice with 50 .mu.l
of cell culture supernatant of transfected cells expressing the
bispecific antibody constructs. The cells are washed twice in PBS
with 2% FCS and binding of the construct is detected with a murine
Penta His antibody (Qiagen; diluted 1:20 in 50 .mu.l PBS with 2%
FCS).
[0412] After washing, bound anti His antibodies are detected with
an Fc gamma-specific antibody (Dianova) conjugated to
phycoerythrin, diluted 1:100 in PBS with 2% FCS. Supernatant of
untransfected cells is used as a negative control.
[0413] Flow cytometry is performed on a FACS-Calibur apparatus, the
CellQuest software is used to acquire and analyze the data (Becton
Dickinson biosciences, Heidelberg). FACS staining and measuring of
the fluorescence intensity are performed as described in Current
Protocols in Immunology (Coligan, Kruisbeek, Margulies, Shevach and
Strober, Wiley-Interscience, 2002).
[0414] Only those constructs that show bispecific binding to human
CD3 as well as to human PSMA and neither bind to the rat PSMA
antigen nor to the mutated rat PSMA antigen with human
membrane-distal epitopes are selected for further use.
2.14 Bioactivity of Bispecific Antibodies Directed at
Membrane-Proximal Target Epitopes of Human PSMA
[0415] Bioactivity of generated bispecific single chain antibodies
is analyzed by chromium 51 (.sup.51Cr) release in vitro
cytotoxicity assays using the CHO cells transfected with human PSMA
described in Example 2.1. As effector cells stimulated human
CD4/CD56 depleted PBMC are used.
[0416] Stimulated human PBMC are obtained as follows:
[0417] A Petri dish (145 mm diameter, Greiner bio-one GmbH,
Kremsmunster) is coated with a commercially available anti-CD3
specific antibody (e.g. OKT3, Orthoclone) in a final concentration
of 1 .mu.g/ml for 1 hour at 37.degree. C. Unbound protein is
removed by one washing step with PBS. The fresh PBMC are isolated
from peripheral blood (30-50 ml human blood) by Ficoll gradient
centrifugation according to standard protocols. 3-5.times.10.sup.7
PBMC are added to the precoated petri dish in 120 ml of RPMI 1640
with stabilized glutamine/10% FCS/IL-2 20 U/ml (Proleukin, Chiron)
and stimulated for 2 days. On the third day the cells are collected
and washed once with RPMI 1640. IL 2 is added to a final
concentration of 20 U/ml and the cells are cultivated again for one
day in the same cell culture medium as above.
[0418] By depletion of CD4+ T cells and CD56+NK cells according to
standard protocols CD8+ cytotoxic T lymphocytes (CTLs) are
enriched.
[0419] Target cells are washed twice with PBS and labeled with 11.1
MBq .sup.51Cr in a final volume of 100 .mu.l RPMI with 50% FCS for
60 minutes at 37.degree. C. Subsequently the labeled target cells
are washed 3 times with 5 ml RPMI and then used in the cytotoxicity
assay. The assay is performed in a 96 well plate in a total volume
of 250 .mu.l supplemented RPMI (as above) with an E:T ratio of
10:1. 1 .mu.g/ml of purified bispecific single chain antibody
molecule and 20 threefold dilutions thereof are applied. The assay
time is 18 hours. Cytotoxicity is measured as relative values of
released chromium in the supernatant related to the difference of
maximum lysis (addition of Triton-X) and spontaneous lysis (without
effector cells). All measurements are done in quadruplicates.
Measurement of chromium activity in the supernatants is performed
with a Wizard 3'' gammacounter (Perkin Elmer Life Sciences GmbH,
Koln, Germany). Analysis of the experimental data is performed with
Prism 4 for Windows (version 4.02, GraphPad Software Inc., San
Diego, Calif., USA). Sigmoidal dose response curves typically have
R.sup.2 values >0.90 as determined by the software. EC50 values
calculated by the analysis program are used for comparison of
bioactivity.
[0420] Only those constructs showing potent recruitment of
cytotoxic activity of effector T cells against target cells
positive for PSMA are selected for further use.
2.15 Generation of CHO Cells Expressing Macaque PSMA
[0421] The cDNA sequence of macaque PSMA is obtained by a set of
five PCRs on cDNA from macaque monkey prostate prepared according
to standard protocols. The following reaction conditions: 1 cycle
at 94.degree. C. for 2 minutes followed by 40 cycles with
94.degree. C. for 1 minute, 52.degree. C. for 1 minute and
72.degree. C. for 1.5 minutes followed by a terminal cycle of
72.degree. C. for 3 minutes and the following primers are used:
TABLE-US-00001 1. forward primer: SEQ ID NO: 228
5'-cactgtggcccaggttcgagg-3' reverse primer: SEQ ID NO: 229
5'-gacataccacacaaattcaatacgg-3' 2. forward primer: SEQ ID NO: 230
5'-gctctgctcgcgccgagatgtgg-3' reverse primer: SEQ ID NO: 231
5'-acgctggacaccacctccagg-3' 3. forward primer: SEQ ID NO: 232
5'-ggttctactgagtgggcagagg-3' reverse primer: SEQ ID NO: 233
5'-acttgttgtggctgcttggagc-3' 4. forward primer: SEQ ID NO: 234
5'-gggtgaagtcctatccagatgg-3' reverse primer: SEQ ID NO: 235
5'-gtgctctgcctgaagcaattcc-3' 5. forward primer: SEQ ID NO: 236
5'-ctcggcttcctcttcgggtgg-3' reverse primer: SEQ ID NO: 237
5'-gcatattcatttgctgggtaacctgg-3'
[0422] Those PCRs generate five overlapping fragments, which are
isolated and sequenced according to standard protocols using the
PCR primers, and thereby provided a portion of the cDNA sequence
coding macaque PSMA from codon 3 to the last codon of the mature
protein. To generate a construct for expression of macaque PSMA a
cDNA fragment is obtained by gene synthesis according to standard
protocols (the cDNA and amino acid sequence of the construct is
listed under SEQ ID NO: 238 and 239). In this construct the coding
sequence of macaque PSMA from amino acid 3 to the last amino acid
of the mature PSMA protein followed by a stop codon is fused in
frame to the coding sequence of the first two amino acids of the
human PSMA protein. The gene synthesis fragment is also designed as
to contain a Kozak site for eukaryotic expression of the construct
and restriction sites at the beginning and the end of the fragment
containing the cDNA. The introduced restriction sites, XbaI at the
5' end and SalI at the 3' end, are utilised in the following
cloning procedures. The gene synthesis fragment is cloned via XbaI
and SalI into a plasmid designated pEF-DHFR (pEF-DHFR is described
in Raum et al. Cancer Immunol Immunother 50 (2001) 141-150)
following standard protocols. The aforementioned procedures are
carried out according to standard protocols (Sambrook, Molecular
Cloning; A Laboratory Manual, 3rd edition, Cold Spring Harbour
Laboratory Press, Cold Spring Harbour, New York (2001)). A clone
with sequence-verified nucleotide sequence is transfected into DHFR
deficient CHO cells for eukaryotic expression of the construct.
Eukaryotic protein expression in DHFR deficient CHO cells is
performed as described by Kaufmann R. J. (1990) Methods Enzymol.
185, 537-566. Gene amplification of the construct is induced by
increasing concentrations of methotrexate (MTX) to a final
concentration of up to 20 nM MTX.
2.16 Flow Cytometric Analysis of Cross-Species Specificity of
Bispecific Antibodies Directed at Membrane-Proximal Target Epitopes
of Human PSMA
[0423] In order to test the cross-species specificity of bispecific
antibodies directed at membrane-proximal target epitopes of human
PSMA the capability of the constructs to bind to macaque PSMA and
macaque CD3, respectively, is investigated by FACS analysis. For
this purpose the macaque PSMA transfected CHO cells as described in
example 2.15 and the macaque T cell line 4119LnPx (kindly provided
by Prof Fickenscher, Hygiene Institute, Virology,
Erlangen-Nuernberg; published in Knappe A, et al., and Fickenscher
H., Blood 2000, 95, 3256-61) are used. 200.000 cells of the
respective cell lines are incubated for 30 min on ice with with 50
.mu.l of cell culture supernatant of transfected cells expressing
the cross-species specific bispecific antibody constructs. The
cells are washed twice in PBS with 2% FCS and binding of the
construct is detected with a murine Penta His antibody (Qiagen;
diluted 1:20 in 50 .mu.l PBS with 2% FCS). After washing, bound
anti His antibodies are detected with an Fc gamma-specific antibody
(Dianova) conjugated to phycoerythrin, diluted 1:100 in PBS with 2%
FCS. Supernatant of untransfected cells is used as a negative
control. Flow cytometry is performed on a FACS-Calibur apparatus,
the CellQuest software is used to acquire and analyze the data
(Becton Dickinson biosciences, Heidelberg).
[0424] FACS staining and measuring of the fluorescence intensity
are performed as described in Current Protocols in Immunology
(Coligan, Kruisbeek, Margulies, Shevach and Strober,
Wiley-Interscience, 2002).
Example 3
3.1. Generation of PSMA- and CD3-Directed Bispecific Single
Antibodies
[0425] Bispecific single chain antibodes comprising either scFv
binding domain P1, P2, P3, P4 or P5 against a PSMA-epitope of
<60 .ANG. membrane-distance or scFv binding domain D1 or D2
against a PSMA-epitope of .gtoreq.60 .ANG. membrane-distance and
the scFv binding domain I2C directed at CD3epsilon on human T cells
were obtained by gene synthesis. The gene synthesis fragments were
designed as to contain first a Kozak site for eukaryotic expression
of the construct, followed by a 19 amino acid immunoglobulin leader
peptide, followed in frame by the coding sequence of the bispecific
single chain antibody, followed in frame by the coding sequence of
a 6 histidine tag and a stop codon. The variable region
arrangements as well as the SEQ ID Nos of the cDNA- and amino acid
sequences are listed in the table 3 below.
TABLE-US-00002 TABLE 3 SEQ ID Formats of protein constructs
(nucl/prot) (N .fwdarw. C) 281/280 PSMA-P1 LH .times. I2C HL
295/294 PSMA-P2 LH .times. I2C HL 309/308 PSMA-P3 LH .times. I2C HL
323/322 PSMA-P4 LH .times. I2C HL 337/336 PSMA-P5 LH .times. I2C HL
351/350 PSMA-D1 LH .times. I2C HL 365/364 PSMA-D2 LH .times. I2C
HL
[0426] The gene synthesis fragments were also designed as to
introduce suitable restriction sites at the beginning (EcoRI) and
at the end of the fragment (Sal I) for cloning of the gene
synthesis fragment into the mammalian cell expression vector
pEF-DHFR (pEF-DHFR is described in Raum et al. Cancer Immunol
Immunother 50 (2001) 141-150). The aforementioned procedures were
carried out according to standard protocols (Sambrook, Molecular
Cloning; A Laboratory Manual, 3rd edition, Cold Spring Harbour
Laboratory Press, Cold Spring Harbour, New York (2001)). A clone
with sequence-verified nucleotide sequence was transfected into
DHFR deficient CHO cells for eukaryotic expression of the
construct. Eukaryotic protein expression in DHFR deficient CHO
cells was performed as described by Kaufmann R. J. (1990) Methods
Enzymol. 185, 537-566. Gene amplification of the construct was
induced by increasing concentrations of methotrexate (MTX) to a
final concentration of up to 20 nM MTX. After two passages of
stationary culture cell culture supernatant was collected and used
in the subsequent experiments.
3.2. Membrane-Distance <60 .ANG. or .gtoreq.60 .ANG. of
PSMA-Epitopes Recognized by I2C-Based PSMA-Directed bscAbs
[0427] Epitope confirmation of PSMA-directed bispecific single
antibodies was carried out by flowcytometry on CHO cells
transfected with (unmutated) human PSMA, unmutated rat PSMA and rat
PSMA mutated to the homologous human amino acid at every mismatched
amino acid position with a membrane-distance of 60 .ANG. as
described in Example 2.
[0428] 200,000 cells of each CHO-transfectant were incubated for 30
min on ice with 50 .mu.l of cell culture supernatant of transfected
cells expressing the PSMA-directed bispecific antibody constructs.
The cells were washed twice in PBS with 2% FCS and binding of the
construct was detected with a murine Penta His antibody (Qiagen;
diluted 1:20 in 50 .mu.l PBS with 2% FCS). After washing, bound
anti His antibodies were detected with an Fc gamma-specific
antibody (Dianova) conjugated to phycoerythrin, diluted 1:100 in
PBS with 2% FCS. Cell culture medium was used as a negative
control. Flowcytometry was performed on a FACS-Calibur apparatus,
the CellQuest software was used to acquire and analyze the data
(Becton Dickinson biosciences, Heidelberg). FACS staining and
measuring of the fluorescence intensity were performed as described
in Current Protocols in Immunology (Coligan, Kruisbeek, Margulies,
Shevach and Strober, Wiley-Interscience, 2002).
[0429] FIG. 4 shows, that PSMA-directed bscAbs P1.times.I2C,
P2.times.I2C, P3.times.I2C, P4.times.I2C and P5.times.I2C bind to
(unmutated) human PSMA but neither to unmutated nor to mutated rat
PSMA and thus confirms a membrane-distance of <60 .ANG. for the
PSMA-epitope of each of these bispecific constructs. By contrast,
PSMA-directed bscAbs D1.times.I2C and D2.times.I2C do not bind to
unmutated rat PSMA but to (unmutated) human and mutated rat PSMA
consistent with PSMA-epitopes of a membrane-distance .gtoreq.60
.ANG..
3.3. Relative T Cell Cytotoxicity Redirected by I2C-Based
PSMA-Directed bscAbs with PSMA-Epitopes of a Membrane-Distance
<60 .ANG. and .gtoreq.60 .ANG.
[0430] T cell cytotoxicity redirected by I2C-based PSMA-directed
bscAbs against CHO cells transfected with human PSMA was measured
in a chromium 51 (.sup.51Cr) release assay. As source of effector T
cells stimulated human CD4/CD56 depleted PBMC were used. Stimulated
human PBMC were obtained as follows: A Petri dish (145 mm diameter,
Greiner bio-one GmbH, Kremsmunster) was coated with a commercially
available anti-CD3 specific antibody (e.g. OKT3, Orthoclone) in a
final concentration of 1 .mu.g/ml for 1 hour at 37.degree. C.
Unbound protein was removed by one washing step with PBS. The fresh
PBMC were isolated from peripheral blood (30-50 ml human blood) by
Ficoll gradient centrifugation according to standard protocols.
3-5.times.10.sup.7 PBMC were added to the precoated petri dish in
120 ml of RPMI 1640 with stabilized glutamine/10% FCS/IL-2 20 U/ml
(Proleukin, Chiron) and stimulated for 2 days. On the third day the
cells were collected and washed once with RPMI 1640. IL-2 was added
to a final concentration of 20 U/ml and the cells were cultured
again for one day in the same cell culture medium as above.
[0431] By depletion of CD4+ T cells and CD56+NK cells according to
standard protocols CD8+ cytotoxic T lymphocytes (CTLs) were
enriched. Target cells were washed twice with PBS and labelled with
11.1 MBq .sup.51Cr in a final volume of 100 .mu.l RPMI with 50% FCS
for 60 minutes at 37.degree. C. Subsequently the labelled target
cells were washed 3 times with 5 ml RPMI and then used in the
cytotoxicity assay. The assay was performed in a 96 well plate in a
total volume of 250 .mu.l supplemented RPMI (as above) with an E:T
cell ratio of 10:1. I2C-based PSMA-directed bscAbs were added as
culture supernatants from transfected CHO cells at different
dilutions. The assay time was 18 hours. Cytotoxicity was measured
as relative values of released chromium related to the difference
of maximum lysis (addition of Triton-X) and spontaneous lysis
(without effector cells). All measurements were carried out in
quadruplicates. Measurement of released chromium activity was
performed with a Wizard 3'' gammacounter (Perkin Elmer Life
Sciences GmbH, Koln, Germany). Analysis of the experimental data
was performed with Prism 4 for Windows (version 4.02, GraphPad
Software Inc., San Diego, Calif., USA). Sigmoidal dose response
curves typically had R.sup.2 values >0.90 as determined by the
software.
[0432] As shown in FIG. 5 all 5 PSMA-directed bscAbs, whose
PSMA-epitopes have a membrane-distance of <60 .ANG. are
substantially more potent in redirecting T cell cytotoxicity than
the other two PSMA-directed bscAbs, whose PSMA-epitopes have a
membrane-distance of .gtoreq.60 .ANG..
4. Generation of Additional Bispecific Single Antibodies Directed
at CD3 and Membrane-Proximal Target Epitopes of Human PSMA
[0433] The human antibody germline VH sequence VH1 1-03
(http://vbase.mrc-cpe.cam.ac.uk/) is chosen as framework context
for CDRH1 (SEQ ID NO 260), CDRH2 (SEQ ID NO 261) and CDRH3 (SEQ ID
NO 262). For VH1 1-03 the following degenerated oligonucleotides
have to be synthesized that overlap in a terminal stretch of
approximately 15-20 nucleotides (to this end every second primer is
an antisense primer):
TABLE-US-00003 5'P6-VH-A-XhoI (SEQ ID NO: 449) CTT GAT CTC GAG TCC
GGC SCT GAG STG RWG AAG CCT GGC GCC TCC GTG AAG RTG TCC TGC AAG GCC
TCC GGC TAC 3'P6-VH-B (SEQ ID NO: 450) CCA TTC CAG CMS CTG GCC GGG
TKY CTG TYT CAC CCA GTG CAT CAC GTA GCC GGT GAA GGT GTA GCC GGA GGC
CTT GCA 5'P6-VH-C (SEQ ID NO: 451) CCC GGC CAG SKG CTG GAA TGG ATS
GGC TAC ATC AAC CCT TAC AAC GAC GTG ACC CGG TAC AAC GGC AAG TTC AAG
3'P6-VH-D (SEQ ID NO: 452) TTC CAT GTA GGC GGT GGA GGM GKA CKT GTC
KCT GGT AAK GGT GRC TYT GCC CTT GAA CTT GCC GTT GTA 5'P6-VH-E (SEQ
ID NO: 453) TCC ACC GCC TAC ATG GAA CTG TCC RGC CTG ASG TCT GAG GAC
ACC GCC GTG TAC TAC TGC GCC AGG GGC 3'P6-VH-F-BstEII (SEQ ID NO:
454) CGA TAC GGT GAC CAG AGT GCC TCT GCC CCA GGA GTC GAA GTA GTA
CCA GTT CTC GCC CCT GGC GCA GTA GTA
[0434] This primer-set spans over the whole VH sequence.
[0435] Within this set primers are mixed in equal amounts (e.g. 1
.mu.l of each primer (primer stocks 20 to 100 .mu.M) to a 20 .mu.l
PCR reaction) and added to a PCR mix consisting of PCR buffer,
nucleotides and Taq polymerase. This mix is incubated at 94.degree.
C. for 3 minutes, 65.degree. C. for 1 minute, 62.degree. C. for 1
minute, 59.degree. C. for 1 minute, 56.degree. C. for 1 minute,
52.degree. C. for 1 minute, 50.degree. C. for 1 minute and at
72.degree. C. for 10 minutes in a PCR cycler. Subsequently the
product is run in an agarose gel electrophoresis and the product of
a size from 200 to 400 isolated from the gel according to standard
methods.
[0436] The VH PCR product is then used as a template for a standard
PCR reaction using primers that incorporate N-terminal and
C-terminal suitable cloning restriction sites. The DNA fragment of
the correct size (for a VH approximately 350 nucleotides) is
isolated by agarose gel electrophoresis according to standard
methods. In this way sufficient VH DNA fragment is amplified.
[0437] The human antibody germline VL sequence VklI A1
(http://vbase.mrc-cpe.cam.ac.uk/) is chosen as framework context
for CDRL1 (SEQ ID NO: 255), CDRL2 (SEQ ID NO: 256) and CDRL3 (SEQ
ID NO: 257). For VklI A1 the following degenerated oligonucleotides
have to be synthesized that overlap in a terminal stretch of
approximately 15-20 nucleotides (to this end every second primer is
an antisense primer):
TABLE-US-00004 5'P6-VL-A-SacI (SEQ ID NO: 455) CTT GAT GAG CTC GTG
ATG ACC CAG TCT CCA SYC TCC CTG SCT GTG ACT CTG GGC CAG CSG GCC TCC
ATC TCT TGC CGG 3'P6-VL-B (SEQ ID NO: 456) CCA GTG CAT GAA GGT GTT
GTC GTA GGA GTC GAT GGA CTC GGA GGC CCG GCA AGA GAT GGA GGC
5'P6-VL-C (SEQ ID NO: 457) ACC TTC ATG CAC TGG TWT CAG CAG ARG CCT
GGC CAG YCT CCT MRC CKG CTG ATC TWC CGG GCC TCT ATC CTG GAA
3'P6-VL-D (SEQ ID NO: 458) CAG GGT GAA GTC GGT GCC GGA GCC AGA GCC
GGA GAA CCG GKC AGG GAY GCC GGA TTC CAG GAT AGA GGC CCG 5'P6-VL-E
(SEQ ID NO: 459) ACC GAC TTC ACC CTG AMA ATC TMC CST GTG GAG GCC
GAS GAC GTG GSC RYC TAC TAC TGC CAC CAG 3'P6-VL-F-BsiWI/SpeI (SEQ
ID NO: 460) ACT CAG ACT AGT CGT ACG CTT GAT TTC CAG CTT GGT CCC TCC
GCC GAA GGT GTA AGG GTC CTC GAT GGA CTG GTG GCA GTA GTA
[0438] This primer-set spans over the whole corresponding VL
sequence.
[0439] Within this set primers are mixed in equal amounts (e.g. 1
.mu.l of each primer (primer stocks 20 to 100 .mu.M) to a 20 .mu.l
PCR reaction) and added to a PCR mix consisting of PCR buffer,
nucleotides and Taq polymerase. This mix is incubated at 94.degree.
C. for 3 minutes, 65.degree. C. for 1 minute, 62.degree. C. for 1
minute, 59.degree. C. for 1 minute, 56.degree. C. for 1 minute,
52.degree. C. for 1 minute, 50.degree. C. for 1 minute and at
72.degree. C. for 10 minutes in a PCR cycler. Subsequently the
product is run in an agarose gel electrophoresis and the product of
a size from 200 to 400 isolated from the gel according to standard
methods.
[0440] The VL PCR product is then used as a template for a standard
PCR reaction using primers that incorporate N-terminal and
C-terminal suitable cloning restriction sites.
[0441] The DNA fragment of the correct size (for a VL approximately
330 nucleotides) is isolated by agarose gel electrophoresis
according to standard methods. In this way sufficient VL DNA
fragment is amplified.
[0442] The final VH1 1-03-based VH PCR product (i.e. the repertoire
of human/humanized VH) is combined with the final VklI A1-based VL
PCR product (i.e. the repertoire of human/humanized VL) in the
phage display vector pComb3H5Bhis. This VH-VL combination forms a
library of functional scFvs from which--after display on
filamentous phage--anti-PSMA binders are selected, screened,
identified and confirmed as described in the following:
[0443] 450 ng of the light chain fragments (SacI-SpeI digested) are
ligated with 1400 ng of the phagemid pComb3H5Bhis (SacI-SpeI
digested; large fragment). The resulting combinatorial antibody
library is then transformed into 300 ul of electrocompetent
Escherichia coli XL1 Blue cells by electroporation (2.5 kV, 0.2 cm
gap cuvette, 25 uFD, 200 Ohm, Biorad gene-pulser) resulting in a
library size of more than 10.sup.7 independent clones. After one
hour of phenotype expression, positive transformants are selected
for carbenicilline resistance encoded by the pComb3H5BHis vector in
100 ml of liquid super broth (SB)-culture over night. Cells are
then harvested by centrifugation and plasmid preparation is carried
out using a commercially available plasmid preparation kit
(Qiagen).
[0444] 2800 ng of this plasmid-DNA containing the VL-library
(XhoI-BstElI digested; large fragment) are ligated with 900 ng of
the heavy chain V-fragments (XhoI-BstElI digested) and again
transformed into two 300 ul aliquots of electrocompetent E. coli
XL1 Blue cells by electroporation (2.5 kV, 0.2 cm gap cuvette, 25
uFD, 200 Ohm) resulting in a total VH-VL scFv (single chain
variable fragment) library size of more than 10.sup.7 independent
clones.
[0445] After phenotype expression and slow adaptation to
carbenicilline, the E. coli cells containing the antibody library
are transferred into SB-carbenicilline (SB with 50 ug/mL
carbenicilline) selection medium. The E. coli cells containing the
antibody library is then infected with an infectious dose of
10.sup.12 particles of helper phage VCSM13 resulting in the
production and secretion of filamentous M13 phage, wherein phage
particle contains single stranded pComb3H5BHis-DNA encoding a
scFv-fragment and displayed the corresponding scFv-protein as a
translational fusion to phage coat protein III. This pool of phages
displaying the antibody library is used for the selection of
antigen binding entities.
[0446] For this purpose the phage library carrying the cloned
scFv-repertoire is harvested from the respective culture
supernatant by PEG8000/NaCl precipitation and centrifugation.
Approximately 10.sup.11 to 10.sup.12 scFv phage particles are
resuspended in 0.4 ml of PBS/0.1% BSA and incubated with 10.sup.5
to 10.sup.7 PSMA-positive human prostate cancer cell line LNCaP
(ATCC No. CRL-1740) for 1 hour on ice under slow agitation. These
LNCaP cells are harvested beforehand by centrifugation, washed in
PBS and resuspended in PBS/1% FCS (containing 0.05% Na Azide). scFv
phage which do not specifically bind to LNCaP cells are eliminated
by up to five washing steps with PBS/1% FCS (containing 0.05% Na
Azide). After washing, binding entities are eluted from the cells
by resuspending the cells in HCl-glycine pH 2.2 (10 min incubation
with subsequent vortexing) and after neutralization with 2 M Tris
pH 12, the eluate is used for infection of a fresh uninfected E.
coli XL1 Blue culture (OD600>0.5). The E. coli culture
containing E. coli cells successfully transduced with a phagemid
copy, encoding a human/humanized scFv-fragment, are again selected
for carbenicilline resistance and subsequently infected with VCMS
13 helper phage to start the second round of antibody display and
in vitro selection. A total of 4 to 5 rounds of selections are
carried out, normally.
[0447] In order to screen for PSMA specific binders plasmid DNA
corresponding to 4 and 5 rounds of panning is isolated from E. coli
cultures after selection. For the production of soluble
scFv-protein, VH-VL-DNA fragments are excised from the plasmids
(XhoI-SpeI). These fragments are cloned via the same restriction
sites into the plasmid pComb3H5BFlag/His differing from the
original pComb3H5BHis in that the expression construct (i.e. the
scFv) includes a Flag-tag (DYKDDDDK) at its C-terminus before the
His6-tag and that phage protein III/N2 domain and protein III/CT
domain had been deleted. After ligation, each pool (different
rounds of panning) of plasmid DNA is transformed into 100 .mu.l
heat shock competent E. coli TG1 or XLI blue and plated onto
carbenicilline LB-agar. Single colonies are picked into 100 .mu.l
of LB carb (50 ug/ml carbenicilline).
[0448] E. coli transformed with pComb3H5BFlag/His containing a VL-
and VH-segment produce soluble scFv in sufficient amounts after
induction with 1 mM IPTG. Due to a suitable signal sequence, the
scFv-chain is exported into the periplasma where it folds into a
functional conformation.
[0449] Single E. coli TG1 bacterial colonies from the
transformation plates are picked for periplasmic small scale
preparations and grown in SB-medium (e.g. 10 ml) supplemented with
20 mM MgCl.sub.2 and carbenicilline 50 .mu.g/ml (and re-dissolved
in PBS (e.g. 1 ml) after harvesting. By four rounds of freezing at
-70.degree. C. and thawing at 37.degree. C., the outer membrane of
the bacteria is destroyed by temperature shock and the soluble
periplasmic proteins including the scFvs are released into the
supernatant. After elimination of intact cells and cell-debris by
centrifugation, the supernatant containing the anti-PSMA scFvs is
collected and used for the identification of PSMA specific binders
as follows:
[0450] Binding of scFvs to PSMA is tested by flow cytometry on the
PSMA-positive human prostate cancer cell line LNCaP (ATCC No.
CRL-1740). A periplasmic small scale preparation as described above
without any grown bacteria is used as negative control.
[0451] For flow cytometry 2.5.times.10.sup.5 cells are incubated
with 50 ul of scFv periplasmic preparation or with 5 .mu.g/ml of
purified scFv in 50 .mu.l PBS with 2% FCS. The binding of scFv is
detected with an anti-His antibody (Penta-His Antibody, BSA free,
Qiagen GmbH, Hilden, FRG) at 2 .mu.g/ml in 50 .mu.l PBS with 2%
FCS. As a second step reagent a R-Phycoerythrin-conjugated affinity
purified F(ab')2 fragment, goat anti-mouse IgG (Fc-gamma fragment
specific), diluted 1:100 in 50 .mu.l PBS with 2% FCS (Dianova,
Hamburg, FRG) is used. The samples are measured on a FACSscan (BD
biosciences, Heidelberg, FRG).
[0452] Single clones are then analyzed for favourable properties
and amino acid sequence. PSMA specific scFvs are converted into
recombinant bispecific single chain antibodies by joining them via
a Gly.sub.4Ser.sub.1-linker with the CD3 specific scFv I2C (SEQ ID
NO: 185) or any other CD3 specific scFv of the invention to result
in constructs with the domain arrangement
VH.sub.PSMA-(Gly.sub.4Ser.sub.1).sub.3-VL.sub.PSMA-Ser.sub.1Gly.sub.4Ser.-
sub.1-VH.sub.CD3-(Gly.sub.4Ser.sub.1).sub.3-VL.sub.CD3 or
alternative domain arrangements such as
VL.sub.PSMA-(Gly.sub.4Ser.sub.1).sub.3-VH.sub.PSMA-Gly.sub.4Ser.sub.1-VH.-
sub.CD3-(Gly.sub.4Ser.sub.1).sub.3-VL.sub.CD3. For expression in
CHO cells the coding sequences of (i) an N-terminal immunoglobulin
heavy chain leader comprising a start codon embedded within a Kozak
consensus sequence and (ii) a C-terminal His.sub.6-tag followed by
a stop codon are both attached in frame to the nucleotide sequence
encoding the bispecific single chain antibodies prior to insertion
of the resulting DNA-fragment as obtained by gene synthesis into
the multiple cloning site of the expression vector pEF-DHFR (Raum
et al. Cancer Immunol Immunother 50 (2001) 141-150). Transfection
of the generated expression plasmids is carried out as described in
Example 3.1. Protein expression and purification of bispecific
antibody constructs, flow cytometric confirmation of binding to CD3
and to membrane-proximal target epitopes of human PSMA as well as
the analysis of bioactivity by cytotoxicity assay are performed as
described in Example 2. All other state of the art procedures are
carried out according to standard protocols (Sambrook, Molecular
Cloning; A Laboratory Manual, 3rd edition, Cold Spring Harbour
Laboratory Press, Cold Spring Harbour, New York (2001)).
[0453] Only those bispecific antibody constructs that bind to CD3
and to membrane-proximal target epitopes of human PSMA and show
potent recruitment of cytotoxic activity of effector T cells
against target cells positive for PSMA are selected for further
use.
Example 4
4.1. Generation of PSMA- and CD3-Directed Bispecific Single Chain
Antibodies
[0454] Bispecific single chain antibodes comprising either scFv
binding domain P6 against a PSMA-epitope of <60 .ANG.
membrane-distance or scFv binding domain D3 against a PSMA-epitope
of .gtoreq.60 .ANG. membrane-distance and the scFv binding domain
I2C directed at CD3epsilon on human T cells were obtained by gene
synthesis. The gene synthesis fragments were designed as to contain
first a Kozak site for eukaryotic expression of the construct,
followed by a 19 amino acid immunoglobulin leader peptide, followed
in frame by the coding sequence of the bispecific single chain
antibody, followed in frame by the coding sequence of a 6 histidine
tag and a stop codon. The variable region arrangements as well as
the SEQ ID Nos of the cDNA- and amino acid sequences are listed in
the table 4 below.
TABLE-US-00005 TABLE 4 SEQ ID Formats of protein constructs
(nucl/prot) (N .fwdarw. C) 267/266 PSMA-P6 LH .times. I2C HL
253/252 PSMA-D3 LH .times. I2C HL
[0455] The gene synthesis fragments were also designed as to
introduce suitable restriction sites at the beginning (EcoRI) and
at the end of the fragment (Sal I) for cloning of the gene
synthesis fragment into the mammalian cell expression vector
pEF-DHFR (pEF-DHFR is described in Raum et al. Cancer Immunol
Immunother 50 (2001) 141-150). The aforementioned procedures were
carried out according to standard protocols (Sambrook, Molecular
Cloning; A Laboratory Manual, 3rd edition, Cold Spring Harbour
Laboratory Press, Cold Spring Harbour, New York (2001)). A clone
with sequence-verified nucleotide sequence was transfected into
DHFR deficient CHO cells for eukaryotic expression of the
construct. Eukaryotic protein expression in DHFR deficient CHO
cells was performed as described by Kaufmann R. J. (1990) Methods
Enzymol. 185, 537-566. Gene amplification of the construct was
induced by increasing concentrations of methotrexate (MTX) to a
final concentration of up to 20 nM MTX. After two passages of
stationary culture cell culture supernatant was collected and used
in the subsequent experiments.
4.2. Membrane-Distance <60 .ANG. or .gtoreq.60 .ANG. of
PSMA-Epitopes Recognized by I2C-Based PSMA-Directed bscAbs
[0456] Epitope confirmation of PSMA-directed bispecific single
antibodies was carried out by flowcytometry on CHO cells
transfected with (unmutated) human PSMA, unmutated rat PSMA and rat
PSMA mutated to the homologous human amino acid at every mismatched
amino acid position with a membrane-distance of .gtoreq.60 .ANG. as
described in Example 2.
[0457] 200,000 cells of each CHO-transfectant were incubated for 30
min on ice with 50 .mu.l of cell culture supernatant of transfected
cells expressing the PSMA-directed bispecific antibody constructs.
The cells were washed twice in PBS with 2% FCS and binding of the
construct was detected with a murine Penta His antibody (Qiagen;
diluted 1:20 in 50 .mu.l PBS with 2% FCS). After washing, bound
anti His antibodies were detected with an Fc gamma-specific
antibody (Dianova) conjugated to phycoerythrin, diluted 1:100 in
PBS with 2% FCS. Cell culture medium was used as a negative
control. Flowcytometry was performed on a FACS-Calibur apparatus,
the CellQuest software was used to acquire and analyze the data
(Becton Dickinson biosciences, Heidelberg). FACS staining and
measuring of the fluorescence intensity were performed as described
in Current Protocols in Immunology (Coligan, Kruisbeek, Margulies,
Shevach and Strober, Wiley-Interscience, 2002).
[0458] FIG. 6 shows, that PSMA-directed bscAb P6.times.I2C binds to
(unmutated) human PSMA but neither to unmutated nor to mutated rat
PSMA and thus confirms a membrane-distance of <60 .ANG. for the
PSMA-epitope of this bispecific construct. By contrast,
PSMA-directed bscAb D3.times.I2C does not bind to unmutated rat
PSMA but to (unmutated) human and mutated rat PSMA consistent with
a PSMA-epitope of a membrane-distance .gtoreq.60 .ANG..
4.3. Relative T Cell Cytotoxicity Redirected by I2C-Based
PSMA-Directed bscAbs with PSMA-Epitopes of a Membrane-Distance
<60 .ANG. and .gtoreq.60 .ANG.
[0459] T cell cytotoxicity redirected by I2C-based PSMA-directed
bscAbs against CHO cells transfected with human PSMA was measured
in a chromium 51 (.sup.51Cr) release assay. As source of effector T
cells stimulated human CD4/CD56 depleted PBMC were used. Stimulated
human PBMC were obtained as follows: A Petri dish (145 mm diameter,
Greiner bio-one GmbH, Kremsmunster) was coated with a commercially
available anti-CD3 specific antibody (e.g. OKT3, Orthoclone) in a
final concentration of 1 .mu.g/ml for 1 hour at 37.degree. C.
Unbound protein was removed by one washing step with PBS. The fresh
PBMC were isolated from peripheral blood (30-50 ml human blood) by
Ficoll gradient centrifugation according to standard protocols.
3-5.times.10.sup.7 PBMC were added to the precoated petri dish in
120 ml of RPMI 1640 with stabilized glutamine/10% FCS/IL-2 20 U/ml
(Proleukin, Chiron) and stimulated for 2 days. On the third day the
cells were collected and washed once with RPMI 1640. IL-2 was added
to a final concentration of 20 U/ml and the cells were cultured
again for one day in the same cell culture medium as above.
[0460] By depletion of CD4+ T cells and CD56+NK cells according to
standard protocols CD8+ cytotoxic T lymphocytes (CTLs) were
enriched. Target cells were washed twice with PBS and labelled with
11.1 MBq .sup.51Cr in a final volume of 100 .mu.l RPMI with 50% FCS
for 60 minutes at 37.degree. C. Subsequently the labelled target
cells were washed 3 times with 5 ml RPMI and then used in the
cytotoxicity assay. The assay was performed in a 96 well plate in a
total volume of 250 .mu.l supplemented RPMI (as above) with an E:T
cell ratio of 10:1. I2C-based PSMA-directed bscAbs were added as
culture supernatants from transfected CHO cells at different
dilutions. The assay time was 18 hours. Cytotoxicity was measured
as relative values of released chromium related to the difference
of maximum lysis (addition of Triton-X) and spontaneous lysis
(without effector cells). All measurements were carried out in
quadruplicates. Measurement of released chromium activity was
performed with a Wizard 3'' gammacounter (Perkin Elmer Life
Sciences GmbH, Koln, Germany). Analysis of the experimental data
was performed with Prism 4 for Windows (version 4.02, GraphPad
Software Inc., San Diego, Calif., USA). Sigmoidal dose response
curves typically had R.sup.2 values >0.90 as determined by the
software. As shown in FIG. 7 the PSMA-directed bscAb P6.times.I2C,
whose PSMA-epitope has a membrane-distance of <60 .ANG. is
substantially more potent in redirecting T cell cytotoxicity than
PSMA-directed bscAb D3.times.I2C, whose PSMA-epitope has a
membrane-distance of .gtoreq.60 .ANG..
Example 5: Crossreactive Binding to Human and Non-Chimpanzee
Primate PSMA and CD3 of I2C-Based bscAbs Against Membrane-Proximal
PSMA-Eptitopes
5.1. Cloning and Expression of Cyno PSMA Antigen on CHO Cells
[0461] The cDNA sequence of macaque PSMA was obtained as described
in Example 2.15 As described above, these PCRs generated five
overlapping fragments, which were isolated and sequenced according
to standard protocols using the PCR primers, and thereby provided a
portion of the cDNA sequence coding macaque PSMA from codon 3 to
the last codon of the mature protein. To generate a construct for
expression of macaque PSMA a cDNA fragment was obtained by gene
synthesis according to standard protocols (the cDNA and amino acid
sequence of the construct is listed under SEQ ID Nos 238 and 239).
In this construct the coding sequence of macaque PSMA from amino
acid 3 to the last amino acid of the mature PSMA protein followed
by a stop codon was fused in frame to the coding sequence of the
first two amino acids of the human PSMA protein. The gene synthesis
fragment was also designed as to contain a Kozak site for
eukaryotic expression of the construct and restriction sites at the
beginning and the end of the fragment containing the cDNA. The
introduced restriction sites, XbaI at the 5' end and SalI at the 3'
end, were utilised in the following cloning procedures. The gene
synthesis fragment was cloned via XbaI and SalI into a plasmid
designated pEF-DHFR following standard protocols. The
aforementioned procedures were carried out according to standard
protocols (Sambrook, Molecular Cloning; A Laboratory Manual, 3rd
edition, Cold Spring Harbour Laboratory Press, Cold Spring Harbour,
New York (2001)). A clone with sequence-verified nucleotide
sequence was transfected into DHFR deficient CHO cells for
eukaryotic expression of the construct. Eukaryotic protein
expression in DHFR deficient CHO cells was performed as described
by Kaufmann R. J. (1990) Methods Enzymol. 185, 537-566. Gene
amplification of the construct was induced by increasing
concentrations of methotrexate (MTX) to a final concentration of up
to 20 nM MTX.
5.2. Flow Cytometric Binding Analysis of I2C-Based bscAbs Against
Membrane-Proximal Eptitopes of Human PSMA on Non-Chimanzee Primate
PSMA and on Human and Non-Chimpanzee Primate CD3
[0462] Binding of bscAbs P1.times.I2C, P2.times.I2C, P3.times.I2C,
P4.times.I2C, P5.times.I2C and P6.times.I2C directed against
membrane-proximal PSMA-epitopes to CHO cells expressing human PSMA
is shown by flowcytometry in Examples 3 and 4.
[0463] Binding of these bscAbs to macaque PSMA as well as to human
and macaque CD3 was analysed by flowcytometry using CHO cells
transfected with macaque PSMA, the human CD3 positive T cell
leukemia cell line HPB-ALL (DSMZ, Braunschweig, ACC483) and the CD3
positive macaque T cell line 4119LnPx (kindly provided by Prof
Fickenscher, Hygiene Institute, Virology, Erlangen-Nuernberg;
published in Knappe A, et al., and Fickenscher H., Blood 2000, 95,
3256-61). Results are shown in FIG. 8. 200,000 cells of the
respective cell population were incubated for 30 min on ice with 50
.mu.l of cell culture supernatant of CHO cells transfected with the
PSMA-directed bispecific antibody constructs. The cells were washed
twice in PBS and binding of the construct was detected with an
unlabeled murine Penta His antibody (Qiagen; diluted 1:20 in 50
.mu.l PBS with 2% FCS). After washing, bound anti His antibodies
were detected with an Fc gamma-specific antibody (Dianova)
conjugated to phycoerythrin, diluted 1:100 in 50 .mu.l PBS with 2%
FCS. Fresh culture medium was used as a negative control.
[0464] Flow cytometry was performed on a FACS-Calibur apparatus,
the CellQuest software was used to acquire and analyze the data
(Becton Dickinson biosciences, Heidelberg). FACS staining and
measuring of the fluorescence intensity were performed as described
in Current Protocols in Immunology (Coligan, Kruisbeek, Margulies,
Shevach and Strober, Wiley-Interscience, 2002).
6. Generation of Bispecific Single Chain Antibodies Directed at
Membrane-Proximal Target Epitopes of Human FAPalpha
6.1 Generation of CHO Cells Expressing Human FAPalpha
[0465] The coding sequence of human FAPalpha as published in
GenBank (Accession number NM_004460) is obtained by gene synthesis
according to standard protocols. The gene synthesis fragment is
designed as to contain first a Kozak site for eukaryotic expression
of the construct followed by the coding sequence of the human
FAPalpha protein and a stop codon (the cDNA and amino acid sequence
of the construct is listed under SEQ ID Nos 366 and 367). The gene
synthesis fragment is also designed as to introduce restriction
sites at the beginning and at the end of the fragment. The
introduced restriction sites, XmaI at the 5' end and SalI at the 3'
end, are utilized in the following cloning procedures. The gene
synthesis fragment is cloned via XmaI and SalI into a plasmid
designated pEF-DHFR (pEF-DHFR is described in Raum et al. Cancer
Immunol Immunother 50 (2001) 141-150) following standard protocols.
The aforementioned procedures are carried out according to standard
protocols (Sambrook, Molecular Cloning; A Laboratory Manual, 3rd
edition, Cold Spring Harbour Laboratory Press, Cold Spring Harbour,
New York (2001)). A clone with sequence-verified nucleotide
sequence is transfected into DHFR deficient CHO cells for
eukaryotic expression of the construct. Eukaryotic protein
expression in DHFR deficient CHO cells is performed as described by
Kaufmann R. J. (1990) Methods Enzymol. 185, 537-566. Gene
amplification of the construct is induced by increasing
concentrations of methotrexate (MTX) to a final concentration of up
to 20 nM MTX.
6.2 Generation of a Soluble Human FAPalpha Fusion Protein
[0466] The coding sequence of human FAPalpha as described in
Example 6.1 and the coding sequence of murine Lag3 as published in
GenBank (Accession number NM_008479) are used for the construction
of an artificial cDNA sequence encoding a soluble fusion protein of
human FAPalpha and murine Lag3. To generate a construct for
expression of the soluble human FAPalpha fusion protein .alpha.
cDNA fragment is obtained by gene synthesis according to standard
protocols (the cDNA and amino acid sequence of the construct is
listed under SEQ ID Nos 368 369). The gene synthesis fragment is
designed as to contain first a Kozak site for eukaryotic expression
of the construct followed by the coding sequence of the murine Lag3
protein from amino acid 1 to 441 corresponding to the signal
peptide and extracellular domains of murine Lag3, followed in frame
by the coding sequence of an artificial
Ser.sub.1-Gly.sub.4-Ser.sub.1-linker, followed in frame by the
coding sequence of the human FAPalpha protein from amino acid 27 to
760 corresponding to the extracellular domains of human FAPalpha,
followed in frame by the coding sequence of an artificial
Ser.sub.1-Gly.sub.1-linker, followed in frame by the coding
sequence of a 6 histidine tag and a stop codon. The gene synthesis
fragment is also designed as to introduce restriction sites at the
beginning and at the end of the fragment. The introduced
restriction sites, SpeI at the 5' end and SalI at the 3' end, are
utilized in the following cloning procedures. The gene synthesis
fragment is cloned via SpeI and SalI into a plasmid designated
pEF-DHFR (pEF-DHFR is described in Raum et al. Cancer Immunol
Immunother 50 (2001) 141-150) following standard protocols. The
aforementioned procedures are all carried out according to standard
protocols (Sambrook, Molecular Cloning; A Laboratory Manual, 3rd
edition, Cold Spring Harbour Laboratory Press, Cold Spring Harbour,
New York (2001)). A clone with sequence-verified nucleotide
sequence is transfected into DHFR deficient CHO cells for
eukaryotic expression of the construct. Eukaryotic protein
expression in DHFR deficient CHO cells is performed as described by
Kaufmann R. J. (1990) Methods Enzymol. 185, 537-566. Gene
amplification of the construct is induced by increasing
concentrations of methotrexate (MTX) to a final concentration of up
to 20 nM MTX. After two passages of stationary culture the cells
are grown in roller bottles with nucleoside-free HyQ PF CHO liquid
soy medium (with 4.0 mM L-Glutamine with 0.1% Pluronic F--68;
HyClone) for 7 days before harvest. The cells are removed by
centrifugation and the supernatant containing the expressed protein
is stored at -20.degree. C. Alternatively a clone of the expression
plasmid with sequence-verified nucleotide sequence is used for
transfection and protein expression in the FreeStyle 293 Expression
System (Invitrogen GmbH, Karlsruhe, Germany) according to the
manufacturer's protocol. Supernatant containing the expressed
protein is obtained, cells are removed by centrifugation and the
supernatant is stored at -20.degree. C. Purification of the soluble
human FAPalpha fusion protein is performed as follows:
[0467] Akta.RTM. Explorer System (GE Health Systems) and
Unicorn.RTM. Software are used for chromatography. Immobilized
metal affinity chromatography ("IMAC") is performed using a
Fractogel EMD Chelate.RTM. (Merck) which is loaded with ZnCl.sub.2
according to the protocol provided by the manufacturer. The column
is equilibrated with buffer A (20 mM sodium phosphate buffer pH
7.2, 0.1 M NaCl) and the cell culture supernatant (500 ml) is
applied to the column (10 ml) at a flow rate of 3 ml/min. The
column is washed with buffer A to remove unbound sample. Bound
protein is eluted using a two step gradient of buffer B (20 mM
sodium phosphate buffer pH 7.2, 0.1 M NaCl, 0.5 M Imidazole)
according to the following procedure:
[0468] Step 1: 20% buffer B in 6 column volumes
[0469] Step 2: 100% buffer B in 6 column volumes
[0470] Eluted protein fractions from step 2 are pooled for further
purification. All chemicals are of research grade and purchased
from Sigma (Deisenhofen) or Merck (Darmstadt).
[0471] Gel filtration chromatography is performed on a HiLoad 16/60
Superdex 200 prep grade column (GE/Amersham) equilibrated with
Equi-buffer (25 mM Citrate, 200 mM Lysine, 5% Glycerol, pH 7.2).
Eluted protein samples (flow rate 1 ml/min) are subjected to
standard SDS-PAGE and Western Blot for detection. Prior to
purification, the column is calibrated for molecular weight
determination (molecular weight marker kit, Sigma MW GF-200).
Protein concentrations are determined using OD280 nm.
6.3 Generation of CHO Cells Expressing Murine FAPalpha
[0472] The sequence of murine FAPalpha (NM_007986, Mus musculus
fibroblast activation protein (Fap), mRNA, National Center for
Biotechnology Information, http://www.ncbi.nlm.nih.gov/entrez) is
used to obtain a synthetic cDNA molecule by gene synthesis
according to standard protocols. The gene synthesis fragment is
designed as to contain first a Kozak site for eukaryotic expression
of the construct followed by the coding sequence of the complete
murine FAPalpha antigen, followed in frame by the coding sequence
of a FLAG-tag and a stop codon (the cDNA and amino acid sequence of
the construct is listed under SEQ ID Nos 370 and 371). An
alternative construct identical to the aforementioned construct
except for a C-terminal 6 Histidine-tag instead of the FLAG-tag is
also generated. The gene synthesis fragment is also designed as to
introduce restriction sites at the 5' end (EcoRI) and at the 3' end
(Sal I) of the cDNA fragment for cloning into the mammalian cell
expression vector pEF-DHFR (pEF-DHFR is described in Raum et al.
Cancer Immunol Immunother 50 (2001) 141-150). The aforementioned
procedures are carried out according to standard protocols
(Sambrook, Molecular Cloning; A Laboratory Manual, 3rd edition,
Cold Spring Harbour Laboratory Press, Cold Spring Harbour, New York
(2001)). A clone with sequence-verified nucleotide sequence is
transfected into DHFR deficient CHO cells for eukaryotic expression
of the construct. Eukaryotic protein expression in DHFR deficient
CHO cells is performed as described by Kaufmann R. J. (1990)
Methods Enzymol. 185, 537-566. Gene amplification for increased
antigen expression is induced by increasing concentrations of
methotrexate (MTX) to a final concentration of up to 20 nM MTX.
Cell surface expression of murine FAPalpha by the generated
transfectants is confirmed by flow cytometric binding analysis
performed as described herein. In the case of the construct with
the 6 Histidine tag a murine Penta His antibody (Qiagen; diluted
1:20 in 50 .mu.l PBS with 2% FCS) was used and detected with an Fc
gamma-specific antibody (Dianova) conjugated to phycoerythrin.
Expression of murine FAPalpha was confirmed as shown in FIG.
10.
6.4 Generation of CHO Cells Expressing a Mutated Human FAPalpha
Antigen with Murine Membrane-Distal Epitopes
[0473] The coding sequence of a mutated human FAPalpha antigen with
murine membrane-distal epitopes is obtained by gene synthesis
according to standard protocols. The gene synthesis fragment is
designed as to contain first a Kozak site for eukaryotic expression
of the construct followed by the coding sequence of the complete
human FAPalpha antigen mutated at 15 specific amino acid positions
as explained below, followed in frame by the coding sequence of a
FLAG-tag and a stop codon (the cDNA and amino acid sequence of the
construct is listed under SEQ ID Nos 372 and 373). All
extracellular amino acids of human FAPalpha mismatching with the
homologous murine sequence, whose alpha C-atoms have a distance of
60 .ANG. from the alpha C-atom of the thirteenth extracellular
amino acid (i.e. the reference aa) as counted from the junction of
transmembrane and extracellular region, are mutated to the
homologous mismatched murine amino acid. This applies to the 15
amino acids that are listed in table 2 and marked in bold. The
homologous mismatched amino acids between human and murine FAPalpha
are identified by sequence alignment as shown in FIG. 9. The gene
synthesis fragment is also designed as to introduce restriction
sites at the 5' end (EcoRI) and at the 3' end (Sal I) of the cDNA
fragment for cloning into the mammalian cell expression vector
pEF-DHFR (pEF-DHFR is described in Raum et al. Cancer Immunol
Immunother 50 (2001) 141-150). Internal restriction sites are
removed by silent mutation of the coding sequence in the gene
synthesis fragment. The aforementioned procedures are carried out
according to standard protocols (Sambrook, Molecular Cloning; A
Laboratory Manual, 3rd edition, Cold Spring Harbour Laboratory
Press, Cold Spring Harbour, New York (2001)). A clone with
sequence-verified nucleotide sequence is transfected into DHFR
deficient CHO cells for eukaryotic expression of the construct.
Eukaryotic protein expression in DHFR deficient CHO cells is
performed as described by Kaufmann R. J. (1990) Methods Enzymol.
185, 537-566. Gene amplification for increased antigen expression
is induced by increasing concentrations of methotrexate (MTX) to a
final concentration of up to 20 nM MTX.
[0474] Cell surface expression of mutated human FAPalpha with
murine membrane-distal epitopes by the generated transfectants is
confirmed by flow cytometric binding analysis performed as
described herein using an anti-FLAG M2 antibody (Sigma-Aldrich,
Inc.; diluted 1:900 in 50 .mu.l PBS with 2% FCS) detected with an
Fc gamma-specific antibody (Dianova) conjugated to phycoerythrin.
Expression of mutated human FAPalpha with murine membrane-distal
epitopes was confirmed as shown in FIG. 10.
6.5 Generation of CHO Cells Expressing a Mutated Murine FAPalpha
Antigen with Human Membrane-Distal Epitopes
[0475] The coding sequence of a mutated murine FAPalpha antigen
with human membrane-distal epitopes is obtained by gene synthesis
according to standard protocols. The gene synthesis fragment is
designed as to contain first a Kozak site for eukaryotic expression
of the construct followed by the coding sequence of the complete
murine FAPalpha antigen mutated at the same 15 specific
extracellular amino acid positions as identified in the foregoing
Example 6.4 to the respective homologous human amino acid, followed
in frame by the coding sequence of a FLAG tag and a stop codon (the
cDNA and amino acid sequence of the construct is listed under SEQ
ID Nos 374 and 375). The gene synthesis fragment is also designed
as to introduce restriction sites at the 5' end (EcoRI) and at the
3' end (Sal I) of the cDNA fragment for cloning into the mammalian
cell expression vector pEF-DHFR (pEF-DHFR is described in Raum et
al. Cancer Immunol Immunother 50 (2001) 141-150). The
aforementioned procedures are carried out according to standard
protocols (Sambrook, Molecular Cloning; A Laboratory Manual, 3rd
edition, Cold Spring Harbour Laboratory Press, Cold Spring Harbour,
New York (2001)). A clone with sequence-verified nucleotide
sequence is transfected into DHFR deficient CHO cells for
eukaryotic expression of the construct. Eukaryotic protein
expression in DHFR deficient CHO cells is performed as described by
Kaufmann R. J. (1990) Methods Enzymol. 185, 537-566. Gene
amplification for increased antigen expression is induced by
increasing concentrations of methotrexate (MTX) to a final
concentration of up to 20 nM MTX.
6.6 Immunization of Mice Using a Soluble Human FAPalpha Fusion
Protein
[0476] Twelve weeks old F1 mice from BALB/c.times.C57BL/6 crossings
are immunized with the soluble human FAPalpha fusion protein as
described in Example 6.2. To this end for each animal 40 .mu.g of
the soluble human FAPalpha fusion protein are mixed with 10 nmol of
a thioate-modified CpG-Oligonucleotide (5'-tccatgacgttcctgatgct-3')
in 300 .mu.l PBS and are injected intraperitoneally. Mice receive
booster immunizations after 21, 42 and optionally 63 days in the
same way. Ten days after the first booster immunization, blood
samples are taken and antibody serum titers against human FAPalpha
are tested by flow cytometry according to standard protocols. To
this end 200.000 cells of the human FAPalpha transfected CHO cells
as described in Example 6.1 are incubated for 30 min on ice with 50
.mu.l of serum of the immunized animals diluted 1:1000 in PBS with
2% FCS. The cells are washed twice in PBS with 2% FCS and binding
of serum antibodies is detected with a mouse Fc gamma-specific
antibody (Dianova) conjugated to phycoerythrin, diluted 1:100 in
PBS with 2% FCS. Serum of the animals obtained prior to
immunization is used as a negative control.
[0477] Flow cytometry is performed on a FACS-Calibur apparatus, the
CellQuest software is used to acquire and analyze the data (Becton
Dickinson biosciences, Heidelberg). FACS staining and measuring of
the fluorescence intensity are performed as described in Current
Protocols in Immunology (Coligan, Kruisbeek, Margulies, Shevach and
Strober, Wiley-Interscience, 2002).
[0478] Animals demonstrating significant serum reactivity against
human FAPalpha as determined by the FACS analysis are used in the
subsequent experiment.
6.7 Generation of an Immune Murine Antibody scFv Library:
Construction of a Combinatorial Antibody Library and Phage
Display
[0479] Three days after the last booster immunization spleen cells
of reactive animals are harvested for the preparation of total RNA
according to standard protocols.
[0480] A library of murine immunoglobulin (Ig) light chain (kappa)
variable region (VK) and Ig heavy chain variable region (VH)
DNA-fragments is constructed by RT-PCR on murine spleen RNA using
VK- and VH specific primers. cDNA is synthesized according to
standard protocols, see example 2.7.
[0481] 450 ng of the kappa light chain fragments (SacI-SpeI
digested) are ligated with 1400 ng of the phagemid pComb3H5Bhis
(SacI-SpeI digested; large fragment). The resulting combinatorial
antibody library is then transformed into 300 .mu.l of
electrocompetent Escherichia coli XL1 Blue cells by electroporation
(2.5 kV, 0.2 cm gap cuvette, 25 .mu.FD, 200 Ohm, Biorad
gene-pulser) resulting in a library size of more than 10.sup.7
independent clones. After one hour of phenotype expression,
positive transformants are selected for carbenicillin resistance
encoded by the pComb3H5BHis vector in 100 ml of liquid super broth
(SB)-culture over night. Cells are then harvested by centrifugation
and plasmid preparation is carried out using a commercially
available plasmid preparation kit (Qiagen).
[0482] 2800 ng of this plasmid-DNA containing the VK-library
(XhoI-BstElI digested; large fragment) are ligated with 900 ng of
the heavy chain V-fragments (XhoI-BstElI digested) and again
transformed into two 300 .mu.l aliquots of electrocompetent E. coli
XL1 Blue cells by electroporation (2.5 kV, 0.2 cm gap cuvette, 25
.mu.FD, 200 Ohm) resulting in a total VH-VK scFv (single chain
variable fragment) library size of more than 10.sup.7 independent
clones.
[0483] After phenotype expression and slow adaptation to
carbenicillin, the E. coli cells containing the antibody library
are transferred into SB-Carbenicillin (SB with 50 .mu.g/mL
carbenicillin) selection medium. The E. coli cells containing the
antibody library are then infected with an infectious dose of
10.sup.12 particles of helper phage VCSM13 resulting in the
production and secretion of filamentous M13 phage, wherein each
phage particle contains single stranded pComb3H5BHis-DNA encoding a
murine scFv-fragment and displays the corresponding scFv-protein as
a translational fusion to phage coat protein III. This pool of
phages displaying the antibody library is later used for the
selection of antigen binding entities.
6.8 Phage Display Based Selection of Membrane-Proximal Target
Binders on CHO Cells Expressing the Mutated Human FAPalpha Antigen
with Murine Membrane-Distal Epitopes
[0484] The phage library carrying the cloned scFv-repertoire is
harvested from the respective culture supernatant by PEG8000/NaCl
precipitation and centrifugation. Approximately 10.sup.11 to
10.sup.12 scFv phage particles are resuspended in 0.4 ml of
PBS/0.1% BSA and incubated with 10.sup.5 to 10.sup.7 CHO cells
expressing the mutated human FAPalpha antigen with murine
membrane-distal epitopes as described in example 6.4 for 1 hour on
ice under slow agitation. These CHO cells are grown beforehand,
harvested by centrifugation, washed in PBS and resuspended in
PBS/1% FCS (containing Na Azide). scFv phage which do not
specifically bind to the CHO cells are eliminated by up to five
washing steps with PBS/1% FCS (containing Na Azide). After washing,
binding entities are eluted from the cells by resuspending the
cells in HCl-glycine pH 2.2 (10 min incubation with subsequent
vortexing) and after neutralization with 2 M Tris pH 12, the eluate
is used for infection of a fresh uninfected E. coli XL1 Blue
culture (OD600>0.5). The E. coli culture containing E. coli
cells successfully transduced with a phagemid copy, encoding a
murine scFv-fragment, are again selected for carbenicillin
resistance and subsequently infected with VCMS 13 helper phage to
start the second round of antibody display and in vitro selection.
Typically a total of 4 to 5 rounds of selections are carried
out.
6.9 Screening for Membrane-Proximal Target Binders on CHO Cells
Expressing the Human FAPalpha Antigen, the Murine FAPalpha Antigen
and the Mutated Murine FAPalpha Antigen with Human Membrane-Distal
Epitopes
[0485] Plasmid DNA corresponding to 4 and 5 rounds of panning is
isolated from E. coli cultures after selection. For the production
of soluble scFv-protein, VH-VL-DNA fragments are excised from the
plasmids (XhoI-SpeI). These fragments are cloned via the same
restriction sites in the plasmid pComb3H5BFlag/His differing from
the original pComb3H5BHis in that the expression construct (e.g.
scFv) includes a Flag-tag (TGDYKDDDDK) between the scFv and the
His6-tag and the additional phage proteins are deleted. After
ligation, each pool (different rounds of panning) of plasmid DNA is
transformed into 100 .mu.l heat shock competent E. coli TG1 or XLI
blue and plated onto carbenicillin LB-agar. Single colonies are
picked into 100 .mu.l of LB carb (LB with 50 .mu.g/ml
carbenicillin).
[0486] After induction with 1 mM IPTG E. coli transformed with
pComb3H5BFlag/His containing a VL- and VH-segment produce soluble
scFv in sufficient amounts. Due to a suitable signal sequence, the
scFv is exported into the periplasma where it folds into a
functional conformation.
[0487] Single E. coli bacterial colonies from the transformation
plates are picked for periplasmic small scale preparations and
grown in SB-medium (e.g. 10 ml) supplemented with 20 mM MgCl.sub.2
and carbenicillin 50 .mu.g/ml (and re-dissolved in PBS (e.g. 1 ml)
after harvesting. A temperature shock is applied by four rounds of
freezing at -70.degree. C. and thawing at 37.degree. C. whereby the
outer membrane of the bacteria is destroyed and the soluble
periplasmic proteins including the scFvs are released into the
supernatant. After elimination of intact cells and cell-debris by
centrifugation, the supernatant containing the murine anti-human
FAPalpha-scFvs is collected and used for further examination.
[0488] Screening of the isolated scFvs for membrane-proximal target
binders is performed by flow cytometry on CHO cells expressing the
human FAPalpha antigen as described in Example 6.1, the murine
FAPalpha antigen as described in Example 6.3 and the mutated murine
FAPalpha antigen with human membrane-distal epitopes as described
in Example 6.5.
[0489] For flow cytometry 2.5.times.10.sup.5 cells of the
respective cell lines are incubated with 50 .mu.l supernatant. The
binding of the constructs is detected with an anti-His antibody
(Penta-His Antibody, BSA free, Qiagen GmbH, Hilden, FRG) at 2
.mu.g/ml in 50 .mu.l PBS with 2% FCS. As a second step reagent an
R-Phycoerythrin-conjugated affinity purified F(ab')2 fragment, goat
anti-mouse IgG (Fc-gamma fragment specific), diluted 1:100 in 50
.mu.l PBS with 2% FCS (Dianova, Hamburg, FRG) is used. The samples
are measured on a FACSscan (BD biosciences, Heidelberg, FRG).
[0490] Only constructs which show binding to CHO cells expressing
the human FAPalpha antigen and do not show binding to CHO cells
expressing the murine FAPalpha antigen and also do not show binding
to CHO cells expressing the mutated murine FAPalpha antigen with
human membrane-distal epitopes are selected for further use.
6.10 Generation of Human/Humanized Equivalents of Non-Human scFvs
to Membrane-Proximal Target Epitopes of Human FAPalpha
[0491] The VH region of a murine anti-FAPalpha scFv to a
membrane-proximal target epitope of human FAPalpha is aligned
against human antibody germline amino acid sequences. The human
antibody germline VH sequence is chosen which has the closest
homology to the non-human VH and a direct alignment of the two
amino acid sequences is performed. There are a number of framework
residues of the non-human VH that differ from the human VH
framework regions ("different framework positions"). Some of these
residues may contribute to the binding and activity of the antibody
to its target.
[0492] To construct a library that contains the murine CDRs and at
every framework position that differs from the chosen human VH
sequence both possible residues (the human and the maternal murine
amino acid residue), degenerated oligonucleotides are synthesized.
These oligonucleotides incorporate at the differing positions the
human residue with a probability of 75% and the murine residue with
a probability of 25%. For one human VH e.g. six of these
oligonucleotides have to be synthesized that overlap in a terminal
stretch of approximately 20 nucleotides. To this end every second
primer is an antisense primer. Restriction sites within the
oligonucleotides needed for later cloning are deleted.
[0493] These primers may have a length of 60 to 90 nucleotides,
depending on the number of primers that are needed to span over the
whole V sequence.
[0494] These e.g. six primers are mixed in equal amounts (e.g. 1
.mu.l of each primer (primer stocks 20 to 100 .mu.M) to a 20 .mu.l
PCR reaction) and added to a PCR mix consisting of PCR buffer,
nucleotides and Taq polymerase. This mix is incubated at 94.degree.
C. for 3 minutes, 65.degree. C. for 1 minute, 62.degree. C. for 1
minute, 59.degree. C. for 1 minute, 56.degree. C. for 1 minute,
52.degree. C. for 1 minute, 50.degree. C. for 1 minute and at
72.degree. C. for 10 minutes in a PCR cycler. Subsequently the
product is run in an agarose gel electrophoresis and the product of
a size from 200 to 400 base pairs isolated from the gel according
to standard methods.
[0495] This PCR product is then used as a template for a standard
PCR reaction using primers that incorporate suitable N-terminal and
C-terminal cloning restriction sites. The DNA fragment of the
correct size (for a VH approximately 350 nucleotides) is isolated
by agarose gel electrophoresis according to standard methods. In
this way sufficient VH DNA fragment is amplified. This VH fragment
is now a pool of VH fragments that have each one a different amount
of human and murine residues at the respective differing framework
positions (pool of humanized VH). The same procedure is performed
for the VL region of the murine anti-FAPalpha scFv to a
membrane-proximal target epitope of human FAPalpha (pool of
humanized VL). The pool of humanized VH is then combined with the
pool of humanized VL in the phage display vector pComb3H5Bhis to
form a library of functional scFvs from which--after display on
filamentous phage--anti-FAPalpha binders to membrane-proximal
target epitopes of human FAPalpha are selected, screened,
identified and confirmed as described above for the parental
non-human (murine) anti-FAPalpha scFv. Single clones are then
analyzed for favorable properties and amino acid sequence. Those
scFvs, which are closest in amino acid sequence homology to human
germline V-segments, are preferred.
[0496] Human/humanized anti-FAPalpha scFvs to membrane-proximal
target epitopes of human FAPalpha are converted into recombinant
bispecific single chain antibodies and further characterized as
follows.
6.11 Generation of I2C-Based Bispecific Single Chain Antibodies
Directed at Membrane-Proximal Target Epitopes of Human FAPalpha
[0497] Anti-FAPalpha scFvs to membrane-proximal target epitopes of
human FAPalpha with favorable properties and amino acid sequence
are converted into recombinant bispecific single chain antibodies
by joining them via a Gly.sub.4Ser.sub.1-linker with the CD3
specific scFv I2C (SEQ ID NO: 185) to result in constructs with the
domain arrangement
VH.sub.FAPalpha-(Gly.sub.4Ser.sub.1).sub.3-VL.sub.FAPalpha-Ser.sub.1Gly.s-
ub.4Ser.sub.1-VH.sub.CD3-(Gly.sub.4Ser.sub.1).sub.3-VL.sub.CD3.
[0498] I2C-based bispecific single chain antibodies directed at
membrane-proximal target epitopes of human FAPalpha were designed
as set out in the following Table 5:
TABLE-US-00006 TABLE 5 Formats of I2C-based bispecific single chain
antibodies directed at membrane-proximal target epitopes of human
FAPalpha SEQ ID Formats of protein constructs (nucl/prot) (N
.fwdarw. C) 820/819 FA19D12HL .times. I2CHL 806/805 FA20H3HL
.times. I2CHL 750/749 FA22A9HL .times. I2CHL 764/763 FA22C11HL
.times. I2CHL 834/833 FA19D9HL .times. I2CHL 778/777 FA22D8HL
.times. I2CHL 792/791 FA22E8HL .times. I2CHL
[0499] Alternatively further constructs with different domain
arrangements can be generated according to standard protocolls. For
expression in CHO cells the coding sequences of (i) an N-terminal
immunoglobulin heavy chain leader comprising a start codon embedded
within a Kozak consensus sequence and (ii) a C-terminal His6-tag
followed by a stop codon are both attached in frame to the
nucleotide sequence encoding the bispecific single chain antibodies
prior to insertion of the resulting DNA-fragment as obtained by
gene synthesis into the multiple cloning site of the expression
vector pEF-DHFR (Raum et al. Cancer Immunol Immunother 50 (2001)
141-150). A clone with sequence-verified nucleotide sequence is
transfected into DHFR deficient CHO cells for eukaryotic expression
of the construct. Eukaryotic protein expression in DHFR deficient
CHO cells is performed as described by Kaufmann R. J. (1990)
Methods Enzymol. 185, 537-566. Gene amplification of the construct
is induced by increasing concentrations of methotrexate (MTX) to a
final concentration of up to 20 nM MTX.
6.12 Expression and Purification of Bispecific Single Chain
Antibody Molecules Directed at Membrane-Proximal Target Epitopes of
Human FAPalpha
[0500] Bispecific single chain antibody molecules are expressed in
Chinese hamster ovary cells (CHO). Eukaryotic protein expression in
DHFR deficient CHO cells is performed as described by Kaufmann R.
J. (1990) Methods Enzymol. 185, 537-566. Gene amplification of the
constructs is induced by addition of increasing concentrations of
MTX up to final concentrations of 20 nM MTX. After two passages of
stationary culture cell culture supernatant is collected and used
in the subsequent experiments. To generate supernatant for
purification after two passages of stationary culture the cells are
grown in roller bottles with nucleoside-free HyQ PF CHO liquid soy
medium (with 4.0 mM L-Glutamine with 0.1% Pluronic F-68; HyClone)
for 7 days before harvest. The cells are removed by centrifugation
and the supernatant containing the expressed protein is stored at
-20.degree. C. Alternatively, constructs are transiently expressed
in HEK 293 cells. Transfection is performed with 293fectin reagent
(Invitrogen, #12347-019) according to the manufacturer's protocol.
Furthermore the constructs are alternatively expressed in
transiently transfected DHFR deficient CHO cells using for example
FuGENE.RTM. HD Transfection Reagent (Roche Diagnostics GmbH, Cat.
No. 04709691001) according to the manufacturer's protocol.
[0501] Akta.RTM. Explorer System (GE Health Systems) and
Unicorn.RTM. Software are used for chromatography. Immobilized
metal affinity chromatography ("IMAC") is performed using a
Fractogel EMD Chelate.RTM. (Merck) which is loaded with ZnCl.sub.2
according to the protocol provided by the manufacturer. The column
is equilibrated with buffer A (20 mM sodium phosphate buffer pH
7.2, 0.1 M NaCl) and the cell culture supernatant (500 ml) is
applied to the column (10 ml) at a flow rate of 3 ml/min. The
column is washed with buffer A to remove unbound sample. Bound
protein is eluted using a two step gradient of buffer B (20 mM
sodium phosphate buffer pH 7.2, 0.1 M NaCl, 0.5 M Imidazole)
according to the following procedure:
[0502] Step 1: 20% buffer B in 6 column volumes
[0503] Step 2: 100% buffer B in 6 column volumes
[0504] Eluted protein fractions from step 2 are pooled for further
purification. All chemicals are of research grade and purchased
from Sigma (Deisenhofen) or Merck (Darmstadt).
[0505] Gel filtration chromatography is performed on a HiLoad 16/60
Superdex 200 prep grade column (GE/Amersham) equilibrated with
Equi-buffer (25 mM Citrate, 200 mM Lysine, 5% Glycerol, pH 7.2).
Eluted protein samples (flow rate 1 ml/min) are subjected to
standard SDS-PAGE and Western Blot for detection. Prior to
purification, the column is calibrated for molecular weight
determination (molecular weight marker kit, Sigma MW GF-200).
Protein concentrations are determined using OD280 nm.
[0506] Purified bispecific single chain antibody protein is
analyzed in SDS PAGE under reducing conditions performed with
pre-cast 4-12% Bis Tris gels (Invitrogen). Sample preparation and
application are performed according to the protocol provided by the
manufacturer. The molecular weight is determined with MultiMark
protein standard (Invitrogen). The gel is stained with colloidal
Coomassie (Invitrogen protocol). The purity of the isolated protein
is typically >95% as determined by SDS-PAGE. The bispecific
single chain antibody has a molecular weight of about 52 kDa under
native conditions as determined by gel filtration in PBS.
[0507] Western Blot is performed using an Optitran.RTM. BA-S83
membrane and the Invitrogen Blot Module according to the protocol
provided by the manufacturer. The antibody used is directed against
the His Tag (Penta His, Qiagen) and a Goat-anti-mouse Ig labeled
with alkaline phosphatase (AP) (Sigma) is used as second step
reagent, and BCIP/NBT (Sigma) as substrate. A band detected at 52
kD corresponds to purified bispecific single chain antibodies.
6.13 Flow Cytometric Binding Analysis of Bispecific Antibodies
Directed at Membrane-Proximal Target Epitopes of Human FAPalpha
[0508] In order to test the functionality of bispecific antibody
constructs regarding the capability to bind to CD3 and to human
FAPalpha, respectively, a FACS analysis is performed. For this
purpose CHO cells transfected with human FAPalpha as described in
Example 6.1 and the human CD3 positive T cell leukemia cell line
HPB-ALL (DSMZ, Braunschweig, ACC483) are used. 200.000 cells of the
respective cell lines are incubated for 30 min on ice with 50 .mu.l
of cell culture supernatant of transfected cells expressing the
bispecific antibody constructs. The cells are washed twice in PBS
with 2% FCS and binding of the construct is detected with a murine
Penta His antibody (Qiagen; diluted 1:20 in 50 .mu.l PBS with 2%
FCS). After washing, bound anti His antibodies are detected with an
Fc gamma-specific antibody (Dianova) conjugated to phycoerythrin,
diluted 1:100 in PBS with 2% FCS. Supernatant of untransfected
cells is used as a negative control.
[0509] Flow cytometry is performed on a FACS-Calibur apparatus, the
CellQuest software is used to acquire and analyze the data (Becton
Dickinson biosciences, Heidelberg). FACS staining and measuring of
the fluorescence intensity are performed as described in Current
Protocols in Immunology (Coligan, Kruisbeek, Margulies, Shevach and
Strober, Wiley-Interscience, 2002).
[0510] Only those constructs that show bispecific binding to human
CD3 as well as to human FAPalpha are selected for further use.
[0511] The bispecific binding of the single chain molecules listed
above was clearly detectable as shown in FIG. 11. In the FACS
analysis all constructs showed binding to human CD3 and human FAPA
compared to the negative control.
6.14 Bioactivity of Bispecific Antibodies Directed at
Membrane-Proximal Target Epitopes of Human FAPalpha
[0512] Bioactivity of generated bispecific single chain antibodies
is analyzed by chromium 51 (.sup.51Cr) release in vitro
cytotoxicity assays using the CHO cells transfected with human
FAPalpha described in Example 6.1. To confirm that significant
bioactivity is only recruited by binding to membrane-proximal
target epitopes of human FAPalpha --in addition--CHO cells
expressing the murine FAPalpha antigen as described in Example 6.3
and CHO cells expressing the mutated human FAPalpha antigen with
murine membrane-distal epitopes as described in Example 6.4 are
used. As effector cells stimulated human CD4/CD56 depleted PBMC are
used.
[0513] Stimulated human PBMC are obtained as follows:
[0514] A Petri dish (145 mm diameter, Greiner bio-one GmbH,
Kremsmunster) is coated with a commercially available anti-CD3
specific antibody (e.g. OKT3, Orthoclone) in a final concentration
of 1 .mu.g/ml for 1 hour at 37.degree. C. Unbound protein is
removed by one washing step with PBS. The fresh PBMC are isolated
from peripheral blood (30-50 ml human blood) by Ficoll gradient
centrifugation according to standard protocols. 3-5.times.10.sup.7
PBMC are added to the precoated petri dish in 120 ml of RPMI 1640
with stabilized glutamine/10% FCS/IL-2 20 U/ml (Proleukin, Chiron)
and stimulated for 2 days. On the third day the cells are collected
and washed once with RPMI 1640. IL 2 is added to a final
concentration of 20 U/ml and the cells are cultivated again for one
day in the same cell culture medium as above.
[0515] By depletion of CD4+ T cells and CD56+NK cells according to
standard protocols CD8+ cytotoxic T lymphocytes (CTLs) are
enriched.
[0516] Target cells are washed twice with PBS and labeled with 11.1
MBq .sup.51Cr in a final volume of 100 .mu.l RPMI with 50% FCS for
60 minutes at 37.degree. C. Subsequently the labeled target cells
are washed 3 times with 5 ml RPMI and then used in the cytotoxicity
assay. The assay is performed in a 96 well plate in a total volume
of 250 .mu.l supplemented RPMI (as above) with an E:T ratio of
10:1. Supernatant of cells expressing the bispecific single chain
antibody molecules in a final concentration of 6,6% and 14
threefold dilutions thereof are applied. The assay time is 18
hours. Cytotoxicity is measured as relative values of released
chromium in the supernatant related to the difference of maximum
lysis (addition of Triton-X) and spontaneous lysis (without
effector cells). All measurements are done in quadruplicates.
Measurement of chromium activity in the supernatants is performed
with a Wizard 3'' gammacounter (Perkin Elmer Life Sciences GmbH,
Koln, Germany). Analysis of the experimental data is performed with
Prism 4 for Windows (version 4.02, GraphPad Software Inc., San
Diego, Calif., USA). Sigmoidal dose response curves typically have
R.sup.2 values >0.90 as determined by the software.
[0517] Only those constructs showing potent recruitment of
cytotoxic activity of effector T cells against target cells
positive for FAPalpha are selected for further use. As shown in
FIG. 12 all of the generated bispecific antibodies directed at
membrane-proximal target epitopes of human FAPalpha demonstrated
cytotoxic activity against human FAPA positive target cells and
target cells positive for the mutated human FAPalpha antigen with
murine membrane-distal epitopes elicited by stimulated human
CD4/CD56 depleted PBMC but did not recruit significant cytotoxic
activity against murine FAPalpha positive target cells. Thereby
specific recruitment of cytotoxic activity via binding to
membrane-proximal target epitopes of human FAPalpha was
confirmed.
6.15 Generation of CHO Cells Expressing Macaque FAPalpha
[0518] The cDNA sequence of macaque FAPalpha is obtained by a set
of four PCRs on cDNA from macaque monkey skin prepared according to
standard protocols. The following reaction conditions: 1 cycle at
94.degree. C. for 3 minutes followed by 40 cycles with 94.degree.
C. for 0.5 minutes, 56.degree. C. for 0.5 minutes and 72.degree. C.
for 3 minutes followed by a terminal cycle of 72.degree. C. for 3
minutes and the following primers are used:
TABLE-US-00007 1. forward primer: SEQ ID NO: 376
5'-cagcttccaactacaaagacagac-3' reverse primer: SEQ ID NO: 377
5'-tttcctcttcataaacccagtctgg-3' 2. forward primer: SEQ ID NO: 378
5'-ttgaaacaaagaccaggagatccacc-3' reverse primer: SEQ ID NO: 379
5'-agatggcaagtaacacacttcttgc-3' 3. forward primer: SEQ ID NO: 380
5'-gaagaaacatctacagaattagcattgg-3' reverse primer: SEQ ID NO: 381
5'-cacatttgaaaagaccagttccagatgc-3' 4. forward primer: SEQ ID NO:
382 5'-agattacagctgtcagaaaattcatagaaatgg-3' reverse primer: SEQ ID
NO: 383 5'-atataaggttttcagattctgatacaggc-3'
[0519] These PCRs generate four overlapping fragments, which are
isolated and sequenced according to standard protocols using the
PCR primers, and thereby provided the cDNA sequence coding macaque
FAPalpha. To generate a construct for expression of macaque
FAPalpha a cDNA fragment is obtained by gene synthesis according to
standard protocols (the cDNA and amino acid sequence of the
construct is listed under SEQ ID Nos 384 and 385). This construct
contains the complete coding sequence of macaque FAPalpha followed
by a stop codon. The gene synthesis fragment is also designed as to
contain a Kozak site for eukaryotic expression of the construct and
restriction sites at the beginning and the end of the fragment
containing the cDNA. The introduced restriction sites, EcoRI at the
5' end and SalI at the 3' end, are utilised in the following
cloning procedures. The gene synthesis fragment is cloned via EcoRI
and SalI into a plasmid designated pEF-DHFR (pEF-DHFR is described
in Raum et al. Cancer Immunol Immunother 50 (2001) 141-150)
following standard protocols. The aforementioned procedures are
carried out according to standard protocols (Sambrook, Molecular
Cloning; A Laboratory Manual, 3rd edition, Cold Spring Harbour
Laboratory Press, Cold Spring Harbour, New York (2001)). A clone
with sequence-verified nucleotide sequence is transfected into DHFR
deficient CHO cells for eukaryotic expression of the construct.
Eukaryotic protein expression in DHFR deficient CHO cells is
performed as described by Kaufmann R. J. (1990) Methods Enzymol.
185, 537-566. Gene amplification of the construct is induced by
increasing concentrations of methotrexate (MTX) to a final
concentration of up to 20 nM MTX.
6.16 Flow Cytometric Analysis of Cross-Species Specificity of
Bispecific Antibodies Directed at Membrane-Proximal Target Epitopes
of Human FAPalpha
[0520] In order to test the cross-species specificity of bispecific
antibodies directed at membrane-proximal target epitopes of human
FAPalpha the capability of the constructs to bind to macaque
FAPalpha and macaque CD3, respectively, is investigated by FACS
analysis. For this purpose the macaque FAPalpha transfected CHO
cells as described in example 6.15 and the macaque T cell line
4119LnPx (kindly provided by Prof Fickenscher, Hygiene Institute,
Virology, Erlangen-Nuernberg; published in Knappe A, et al., and
Fickenscher H., Blood 2000, 95, 3256-61) are used. 200.000 cells of
the respective cell lines are incubated for 30 min on ice with with
50 .mu.l of cell culture supernatant of transfected cells
expressing the cross-species specific bispecific antibody
constructs. The cells are washed twice in PBS with 2% FCS and
binding of the construct is detected with a murine Penta His
antibody (Qiagen; diluted 1:20 in 50 .mu.l PBS with 2% FCS). After
washing, bound anti His antibodies are detected with an Fc
gamma-specific antibody (Dianova) conjugated to phycoerythrin,
diluted 1:100 in PBS with 2% FCS. Supernatant of untransfected
cells is used as a negative control.
[0521] Flow cytometry is performed on a FACS-Calibur apparatus, the
CellQuest software is used to acquire and analyze the data (Becton
Dickinson biosciences, Heidelberg). FACS staining and measuring of
the fluorescence intensity are performed as described in Current
Protocols in Immunology (Coligan, Kruisbeek, Margulies, Shevach and
Strober, Wiley-Interscience, 2002).
[0522] The cross-species specific binding of the single chain
molecules listed above was clearly detectable as shown in FIG. 11.
In the FACS analysis all constructs showed binding to macaque CD3
and macaque FAPA compared to the negative control.
7. Generation of Bispecific Single Chain Antibodies Directed at
Membrane-Proximal Target Epitopes of Human c-MET 7.1 Generation of
CHO Cells Expressing Human c-MET
[0523] The coding sequence of human c-MET as published in GenBank
(Accession number NM_000245) is obtained by gene synthesis
according to standard protocols. The gene synthesis fragment is
designed as to contain first a Kozak site for eukaryotic expression
of the construct followed by the coding sequence of the human c-MET
protein and a stop codon (the cDNA and amino acid sequence of the
construct is listed under SEQ ID Nos 368 and 387). The gene
synthesis fragment is also designed as to introduce restriction
sites at the beginning and at the end of the fragment. The
introduced restriction sites, EcoRI at the 5' end and SalI at the
3' end, are utilized in the following cloning procedures. Internal
restriction sites are removed by silent mutation of the coding
sequence in the gene synthesis fragment. The gene synthesis
fragment is cloned via EcoRI and SalI into a plasmid designated
pEF-DHFR (pEF-DHFR is described in Raum et al. Cancer Immunol
Immunother 50 (2001) 141-150) following standard protocols. The
aforementioned procedures are carried out according to standard
protocols (Sambrook, Molecular Cloning; A Laboratory Manual, 3rd
edition, Cold Spring Harbour Laboratory Press, Cold Spring Harbour,
New York (2001)). A clone with sequence-verified nucleotide
sequence is transfected into DHFR deficient CHO cells for
eukaryotic expression of the construct. Eukaryotic protein
expression in DHFR deficient CHO cells is performed as described by
Kaufmann R. J. (1990) Methods Enzymol. 185, 537-566. Gene
amplification of the construct is induced by increasing
concentrations of methotrexate (MTX) to a final concentration of up
to 20 nM MTX.
7.2 Generation of a Soluble Human c-MET Fusion Protein
[0524] The modified coding sequence of human c-MET as described in
Example 7.1 is used for the construction of an artificial cDNA
sequence encoding a soluble fusion protein of human c-MET and
murine IgG1 Fc. To generate a construct for expression of the
soluble human c-MET fusion protein .alpha. cDNA fragment is
obtained by gene synthesis according to standard protocols (the
cDNA and amino acid sequence of the construct is listed under SEQ
ID Nos 388 and 389). The gene synthesis fragment is designed as to
contain first a Kozak site for eukaryotic expression of the
construct followed by the coding sequence of the human c-MET
protein from amino acid 1 to 932 corresponding to the signal
peptide and extracellular domains of human c-MET, followed in frame
by the coding sequence of an artificial
Ser.sub.1-Gly.sub.4-Ser.sub.1-linker, followed in frame by the
coding sequence of the hinge region and Fc gamma portion of murine
IgG1, followed in frame by the coding sequence of a 6 histidine tag
and a stop codon. The gene synthesis fragment is also designed as
to introduce restriction sites at the beginning and at the end of
the fragment. The introduced restriction sites, EcoRI at the 5' end
and SalI at the 3' end, are utilized in the following cloning
procedures. The gene synthesis fragment is cloned via EcoRI and
SalI into a plasmid designated pEF-DHFR (pEF-DHFR is described in
Raum et al. Cancer Immunol Immunother 50 (2001) 141-150) following
standard protocols. The aforementioned procedures are all carried
out according to standard protocols (Sambrook, Molecular Cloning; A
Laboratory Manual, 3rd edition, Cold Spring Harbour Laboratory
Press, Cold Spring Harbour, New York (2001)). A clone with
sequence-verified nucleotide sequence is transfected into DHFR
deficient CHO cells for eukaryotic expression of the construct.
Eukaryotic protein expression in DHFR deficient CHO cells is
performed as described by Kaufmann R. J. (1990) Methods Enzymol.
185, 537-566. Gene amplification of the construct is induced by
increasing concentrations of methotrexate (MTX) to a final
concentration of up to 20 nM MTX. After two passages of stationary
culture the cells are grown in roller bottles with nucleoside-free
HyQ PF CHO liquid soy medium (with 4.0 mM L-Glutamine with 0.1%
Pluronic F--68; HyClone) for 7 days before harvest. The cells are
removed by centrifugation and the supernatant containing the
expressed protein is stored at -20.degree. C. Alternatively a clone
of the expression plasmid with sequence-verified nucleotide
sequence is used for transfection and protein expression in the
FreeStyle 293 Expression System (Invitrogen GmbH, Karlsruhe,
Germany) according to the manufacturer's protocol. Supernatant
containing the expressed protein is obtained, cells are removed by
centrifugation and the supernatant is stored at -20.degree. C.
[0525] For purification of the soluble human c-MET fusion protein
.alpha. goat anti-mouse Fc affinity column is prepared according to
standard protocols using a commercially available affinity purified
goat anti-mouse IgG Fc fragment specific antibody with minimal
cross-reaction to human, bovine and horse serum proteins (Jackson
ImmunoResearch Europe Ltd.). Using this affinity column the fusion
protein is isolated out of cell culture supernatant on an Akta
Explorer System (GE Amersham) and eluted by citric acid. The eluate
is neutralized and concentrated.
7.3 Generation of CHO Cells Expressing Murine c-MET
[0526] The sequence of murine c-MET (NM_008591 Mus musculus met
proto-oncogene (Met), mRNA, National Center for Biotechnology
Information, http://www.ncbi.nlm.nih.gov/entrez) is used to obtain
a synthetic cDNA molecule by gene synthesis according to standard
protocols. The gene synthesis fragment is designed as to contain
the coding sequence of an immunoglobulin heavy chain leader
comprising a start codon embedded within a Kozak consensus
sequence, followed in frame by the coding sequence of a FLAG tag,
followed in frame by the complete coding sequence of the mature
murine c-MET (the cDNA and amino acid sequence of the construct is
listed under SEQ ID Nos 390 and 391). The gene synthesis fragment
is also designed as to introduce restriction sites at the 5' end
(EcoRI) and at the 3' end (Sal I) of the cDNA fragment for cloning
into the mammalian cell expression vector pEF-DHFR (pEF-DHFR is
described in Raum et al. Cancer Immunol Immunother 50 (2001)
141-150) Internal restriction sites are removed by silent mutation
of the coding sequence in the gene synthesis fragment. The
aforementioned procedures are carried out according to standard
protocols (Sambrook, Molecular Cloning; A Laboratory Manual, 3rd
edition, Cold Spring Harbour Laboratory Press, Cold Spring Harbour,
New York (2001)). A clone with sequence-verified nucleotide
sequence is transfected into DHFR deficient CHO cells for
eukaryotic expression of the construct. Eukaryotic protein
expression in DHFR deficient CHO cells is performed as described by
Kaufmann R. J. (1990) Methods Enzymol. 185, 537-566. Gene
amplification for increased antigen expression is induced by
increasing concentrations of methotrexate (MTX) to a final
concentration of up to 20 nM MTX.
7.4 Generation of CHO Cells Expressing a Mutated Human c-MET
Antigen with Murine Membrane-Distal Epitopes
[0527] The coding sequence of a mutated human c-MET antigen with
murine membrane-distal epitopes is obtained by gene synthesis
according to standard protocols. The gene synthesis fragment is
designed as to contain the coding sequence of an immunoglobulin
heavy chain leader comprising a start codon embedded within a Kozak
consensus sequence, followed in frame by the coding sequence of a
FLAG tag, followed in frame by the coding sequence of the
alpha-chain of the sema domain of mature murine c-MET followed in
frame by human c-MET from the beta-chain of the sema domain to the
stop codon (the cDNA and amino acid sequence of the construct is
listed under SEQ ID Nos 392 and 393). The gene synthesis fragment
is also designed as to introduce restriction sites at the 5' end
(EcoRI) and at the 3' end (Sal I) of the cDNA fragment for cloning
into the mammalian cell expression vector pEF-DHFR (pEF-DHFR is
described in Raum et al. Cancer Immunol Immunother 50 (2001)
141-150). Internal restriction sites are removed by silent mutation
of the coding sequence in the gene synthesis fragment. The
aforementioned procedures are carried out according to standard
protocols (Sambrook, Molecular Cloning; A Laboratory Manual, 3rd
edition, Cold Spring Harbour Laboratory Press, Cold Spring Harbour,
New York (2001)). A clone with sequence-verified nucleotide
sequence is transfected into DHFR deficient CHO cells for
eukaryotic expression of the construct. Eukaryotic protein
expression in DHFR deficient CHO cells is performed as described by
Kaufmann R. J. (1990) Methods Enzymol. 185, 537-566. Gene
amplification for increased antigen expression is induced by
increasing concentrations of methotrexate (MTX) to a final
concentration of up to 20 nM MTX.
7.5 Generation of CHO Cells Expressing a Mutated Murine c-MET
Antigen with Human Membrane-Distal Epitopes
[0528] The coding sequence of a mutated murine c-MET antigen with
human membrane-distal epitopes is obtained by gene synthesis
according to standard protocols. The gene synthesis fragment is
designed as to contain the coding sequence of an immunoglobulin
heavy chain leader comprising a start codon embedded within a Kozak
consensus sequence, followed in frame by the coding sequence of a
FLAG tag, followed in frame by the coding sequence of the
alpha-chain of the sema domain of mature human c-MET, followed in
frame by murine c-MET from the beta-chain of the sema domain to the
stop codon (the cDNA and amino acid sequence of the construct is
listed under SEQ ID Nos 394 and 395). The gene synthesis fragment
is also designed as to introduce restriction sites at the 5' end
(EcoRI) and at the 3' end (Sal I) of the cDNA fragment for cloning
into the mammalian cell expression vector pEF-DHFR (pEF-DHFR is
described in Raum et al. Cancer Immunol Immunother 50 (2001)
141-150). Internal restriction sites are removed by silent mutation
of the coding sequence in the gene synthesis fragment. The
aforementioned procedures are carried out according to standard
protocols (Sambrook, Molecular Cloning; A Laboratory Manual, 3rd
edition, Cold Spring Harbour Laboratory Press, Cold Spring Harbour,
New York (2001)). A clone with sequence-verified nucleotide
sequence is transfected into DHFR deficient CHO cells for
eukaryotic expression of the construct. Eukaryotic protein
expression in DHFR deficient CHO cells is performed as described by
Kaufmann R. J. (1990) Methods Enzymol. 185, 537-566. Gene
amplification for increased antigen expression is induced by
increasing concentrations of methotrexate (MTX) to a final
concentration of up to 20 nM MTX.
7.6 Immunization of Mice Using a Soluble Human c-MET Fusion
Protein
[0529] Twelve weeks old F1 mice from BALB/c.times.C57BL/6 crossings
are immunized with the soluble human c-MET fusion protein as
described in Example 7.2. To this end for each animal 40 .mu.g of
the soluble human c-MET fusion protein are mixed with 10 nmol of a
thioate-modified CpG-Oligonucleotide (5'-tccatgacgttcctgatgct-3')
in 300 .mu.l PBS and are injected intraperitoneally. Mice receive
booster immunizations after 21, 42 and optionally 63 days in the
same way. Ten days after the first booster immunization, blood
samples are taken and antibody serum titers against human c-MET are
tested by flow cytometry according to standard protocols. To this
end 200.000 cells of the human c-MET transfected CHO cells as
described in Example 7.17 are incubated for 30 min on ice with 50
.mu.l of serum of the immunized animals diluted 1:1000 in PBS with
2% FCS. The cells are washed twice in PBS with 2% FCS and binding
of serum antibodies is detected with an mouse Fc gamma-specific
antibody (Dianova) conjugated to phycoerythrin, diluted 1:100 in
PBS with 2% FCS. Serum of the animals obtained prior to
immunization is used as a negative control.
[0530] Flow cytometry is performed on a FACS-Calibur apparatus, the
CellQuest software is used to acquire and analyze the data (Becton
Dickinson biosciences, Heidelberg). FACS staining and measuring of
the fluorescence intensity are performed as described in Current
Protocols in Immunology (Coligan, Kruisbeek, Margulies, Shevach and
Strober, Wiley-Interscience, 2002).
[0531] Animals demonstrating significant serum reactivity against
human c-MET as determined by the FACS analysis are used in the
subsequent experiment.
7.7 Generation of an Immune Murine Antibody scFv Library:
Construction of a Combinatorial Antibody Library and Phage
Display
[0532] Three days after the last booster immunization spleen cells
of reactive animals are harvested for the preparation of total RNA
according to standard protocols.
[0533] A library of murine immunoglobulin (Ig) light chain (kappa)
variable region (VK) and Ig heavy chain variable region (VH)
DNA-fragments is constructed by RT-PCR on murine spleen RNA using
VK- and VH specific primers. cDNA is synthesized according to
standard protocols, see example 2.7.
[0534] 450 ng of the kappa light chain fragments (SacI-SpeI
digested) are ligated with 1400 ng of the phagemid pComb3H5Bhis
(SacI-SpeI digested; large fragment). The resulting combinatorial
antibody library is then transformed into 300 .mu.l of
electrocompetent Escherichia coli XL1 Blue cells by electroporation
(2.5 kV, 0.2 cm gap cuvette, 25 .mu.FD, 200 Ohm, Biorad
gene-pulser) resulting in a library size of more than 10.sup.7
independent clones. After one hour of phenotype expression,
positive transformants are selected for carbenicillin resistance
encoded by the pComb3H5BHis vector in 100 ml of liquid super broth
(SB)-culture over night. Cells are then harvested by centrifugation
and plasmid preparation is carried out using a commercially
available plasmid preparation kit (Qiagen).
[0535] 2800 ng of this plasmid-DNA containing the VK-library
(XhoI-BstElI digested; large fragment) are ligated with 900 ng of
the heavy chain V-fragments (XhoI-BstElI digested) and again
transformed into two 300 .mu.l aliquots of electrocompetent E. coli
XL1 Blue cells by electroporation (2.5 kV, 0.2 cm gap cuvette, 25
.mu.FD, 200 Ohm) resulting in a total VH-VK scFv (single chain
variable fragment) library size of more than 10.sup.7 independent
clones.
[0536] After phenotype expression and slow adaptation to
carbenicillin, the E. coli cells containing the antibody library
are transferred into SB-Carbenicillin (SB with 50 .mu.g/mL
carbenicillin) selection medium. The E. coli cells containing the
antibody library are then infected with an infectious dose of
10.sup.12 particles of helper phage VCSM13 resulting in the
production and secretion of filamentous M13 phage, wherein each
phage particle contains single stranded pComb3H5BHis-DNA encoding a
murine scFv-fragment and displays the corresponding scFv-protein as
a translational fusion to phage coat protein III. This pool of
phages displaying the antibody library is later used for the
selection of antigen binding entities.
7.8 Phage Display Based Selection of Membrane-Proximal Target
Binders on CHO Cells Expressing the Mutated Human c-MET Antigen
with Murine Membrane-Distal Epitopes
[0537] The phage library carrying the cloned scFv-repertoire is
harvested from the respective culture supernatant by PEG8000/NaCl
precipitation and centrifugation. Approximately 10.sup.11 to
10.sup.12 scFv phage particles are resuspended in 0.4 ml of
PBS/0.1% BSA and incubated with 10.sup.5 to 10.sup.7 CHO cells
expressing the mutated human c-MET antigen with murine
membrane-distal epitopes as described in example 7.17 for 1 hour on
ice under slow agitation. These CHO cells are grown beforehand,
harvested by centrifugation, washed in PBS and resuspended in
PBS/1% FCS (containing Na Azide). scFv phage which do not
specifically bind to the CHO cells are eliminated by up to five
washing steps with PBS/1% FCS (containing Na Azide). After washing,
binding entities are eluted from the cells by resuspending the
cells in HCl-glycine pH 2.2 (10 min incubation with subsequent
vortexing) and after neutralization with 2 M Tris pH 12, the eluate
is used for infection of a fresh uninfected E. coli XL1 Blue
culture (OD600>0.5). The E. coli culture containing E. coli
cells successfully transduced with a phagemid copy, encoding a
murine scFv-fragment, are again selected for carbenicillin
resistance and subsequently infected with VCMS 13 helper phage to
start the second round of antibody display and in vitro selection.
Typically a total of 4 to 5 rounds of selections are carried
out.
7.9 Screening for Membrane-Proximal Target Binders on CHO Cells
Expressing the Human c-MET Antigen, the Murine c-MET Antigen, the
Mutated Human c-MET Antigen with Murine Membrane-Distal Epitopes
and the Mutated Murine c-MET Antigen with Human Membrane-Distal
Epitopes
[0538] Plasmid DNA corresponding to 4 and 5 rounds of panning is
isolated from E. coli cultures after selection. For the production
of soluble scFv-protein, VH-VL-DNA fragments are excised from the
plasmids (XhoI-SpeI). These fragments are cloned via the same
restriction sites in the plasmid pComb3H5BFlag/His differing from
the original pComb3H5BHis in that the expression construct (e.g.
scFv) includes a Flag-tag (TGDYKDDDDK) between the scFv and the
His6-tag and the additional phage proteins are deleted. After
ligation, each pool (different rounds of panning) of plasmid DNA is
transformed into 100 .mu.l heat shock competent E. coli TG1 or XLI
blue and plated onto carbenicillin LB-agar. Single colonies are
picked into 100 .mu.l of LB carb (LB with 50 .mu.g/ml
carbenicillin).
[0539] After induction with 1 mM IPTG E. coli transformed with
pComb3H5BFlag/His containing a VL- and VH-segment produce soluble
scFv in sufficient amounts. Due to a suitable signal sequence, the
scFv is exported into the periplasma where it folds into a
functional conformation.
[0540] Single E. coli bacterial colonies from the transformation
plates are picked for periplasmic small scale preparations and
grown in SB-medium (e.g. 10 ml) supplemented with 20 mM MgCl.sub.2
and carbenicillin 50 .mu.g/ml (and re-dissolved in PBS (e.g. 1 ml)
after harvesting. A temperature shock is applied by four rounds of
freezing at -70.degree. C. and thawing at 37.degree. C. whereby the
outer membrane of the bacteria is destroyed and the soluble
periplasmic proteins including the scFvs are released into the
supernatant. After elimination of intact cells and cell-debris by
centrifugation, the supernatant containing the murine anti-human
c-MET-scFvs is collected and used for further examination.
[0541] Screening of the isolated scFvs for membrane-proximal target
binders is performed by flow cytometry on CHO cells expressing the
human c-MET antigen as described in Example 7.17, the murine c-MET
antigen as described in Example 7.17, the mutated human c-MET
antigen with murine membrane-distal epitopes as described in
Example 7.17 and the mutated murine c-MET antigen with human
membrane-distal epitopes as described in Example 7.17.
[0542] For flow cytometry 2.5.times.10.sup.5 cells of the
respective cell lines are incubated with 50 .mu.l supernatant. The
binding of the constructs is detected with an anti-His antibody
(Penta-His Antibody, BSA free, Qiagen GmbH, Hilden, FRG) at 2
.mu.g/ml in 50 .mu.l PBS with 2% FCS. As a second step reagent a
R-Phycoerythrin-conjugated affinity purified F(ab')2 fragment, goat
anti-mouse IgG (Fc-gamma fragment specific), diluted 1:100 in 50
.mu.l PBS with 2% FCS (Dianova, Hamburg, FRG) is used. The samples
are measured on a FACSscan (BD biosciences, Heidelberg, FRG).
[0543] Only constructs which show binding to CHO cells expressing
the human c-MET antigen and show binding to CHO cells expressing
the mutated human c-MET antigen with murine membrane-distal
epitopes and do not show binding to CHO cells expressing the murine
c-MET antigen and also do not show binding to CHO cells expressing
the mutated murine c-MET antigen with human membrane-distal
epitopes are selected for further use.
[0544] scFv specific for membrane proximal epitopes of human cMET
were generated as described above and designated as set out in the
following Table 6:
TABLE-US-00008 TABLE 6 Designation of single chain antibody
fragments SEQ ID (nucl/prot) Designation 734/733 ME06F2HL 720/719
ME06E10HL 706/705 ME06D2HL 692/691 ME06D1HL 664/663 ME06C7HL
650/649 ME06C6HL 678/677 ME06B7HL 636/635 ME05F6HL 622/621 ME05B7HL
608/607 ME99B1HL 594/593 ME75H6HL
[0545] Membrane-proximal target binding of the single chain
molecules listed above was clearly detectable as shown in FIG. 16.
In the FACS analysis all constructs showed binding to the human
c-MET antigen and showed binding to the mutated human c-MET antigen
with murine membrane-distal epitopes and did not show binding to
the murine c-MET antigen and did also not show binding to the
mutated murine c-MET antigen with human membrane-distal epitopes as
compared to the negative control.
7.10 Generation of Human/Humanized Equivalents of Non-Human scFvs
to Membrane-Proximal Target Epitopes of Human c-MET
[0546] The VH region of a murine anti-c-MET scFv to a
membrane-proximal target epitope of human c-MET is aligned against
human antibody germline amino acid sequences. The human antibody
germline VH sequence is chosen which has the closest homology to
the non-human VH and a direct alignment of the two amino acid
sequences is performed. There are a number of framework residues of
the non-human VH that differ from the human VH framework regions
("different framework positions"). Some of these residues may
contribute to the binding and activity of the antibody to its
target.
[0547] To construct a library that contains the murine CDRs and at
every framework position that differs from the chosen human VH
sequence both possible residues (the human and the maternal murine
amino acid residue), degenerated oligonucleotides are synthesized.
These oligonucleotides incorporate at the differing positions the
human residue with a probability of 75% and the murine residue with
a probability of 25%. For one human VH e.g. six of these
oligonucleotides have to be synthesized that overlap in a terminal
stretch of approximately 20 nucleotides. To this end every second
primer is an antisense primer. Restriction sites within the
oligonucleotides needed for later cloning are deleted.
[0548] These primers may have a length of 60 to 90 nucleotides,
depending on the number of primers that are needed to span over the
whole V sequence.
[0549] These e.g. six primers are mixed in equal amounts (e.g. 1
.mu.l of each primer (primer stocks 20 to 100 .mu.M) to a 20 .mu.l
PCR reaction) and added to a PCR mix consisting of PCR buffer,
nucleotides and Taq polymerase. This mix is incubated at 94.degree.
C. for 3 minutes, 65.degree. C. for 1 minute, 62.degree. C. for 1
minute, 59.degree. C. for 1 minute, 56.degree. C. for 1 minute,
52.degree. C. for 1 minute, 50.degree. C. for 1 minute and at
72.degree. C. for 10 minutes in a PCR cycler. Subsequently the
product is run in an agarose gel electrophoresis and the product of
a size from 200 to 400 base pairs isolated from the gel according
to standard methods.
[0550] This PCR product is then used as a template for a standard
PCR reaction using primers that incorporate suitable N-terminal and
C-terminal cloning restriction sites.
[0551] The DNA fragment of the correct size (for a VH approximately
350 nucleotides) is isolated by agarose gel electrophoresis
according to standard methods. In this way sufficient VH DNA
fragment is amplified. This VH fragment is now a pool of VH
fragments that have each one a different amount of human and murine
residues at the respective differing framework positions (pool of
humanized VH). The same procedure is performed for the VL region of
the murine anti-c-MET scFv to a membrane-proximal target epitope of
human c-MET (pool of humanized VL).
[0552] The pool of humanized VH is then combined with the pool of
humanized VL in the phage display vector pComb3H5Bhis to form a
library of functional scFvs from which--after display on
filamentous phage--anti-c-MET binders to membrane-proximal target
epitopes of human c-MET are selected, screened, identified and
confirmed as described above for the parental non-human (murine)
anti-c-MET scFv. Single clones are then analyzed for favorable
properties and amino acid sequence. Those scFvs, which are closest
in amino acid sequence homology to human germline V-segments, are
preferred.
[0553] Human/humanized anti-c-MET scFvs to membrane-proximal target
epitopes of human c-MET are converted into recombinant bispecific
single chain antibodies and further characterized as follows.
7.11 Generation of I2C-Based Bispecific Single Chain Antibodies
Directed at Membrane-Proximal Target Epitopes of Human c-MET
[0554] Anti-c-MET scFvs to membrane-proximal target epitopes of
human c-MET with favorable properties and amino acid sequence are
converted into recombinant bispecific single chain antibodies by
joining them via a Gly.sub.4Ser.sub.1-linker with the CD3 specific
scFv I2C (SEQ ID NO: 185) to result in constructs with the domain
arrangement
VH.sub.c-MET-(Gly.sub.4Ser.sub.1).sub.3-VL.sub.c-MET-Ser.sub.1Gly.sub.4Se-
r.sub.1-VH.sub.CD3-(Gly.sub.4Ser.sub.1).sub.3-VL.sub.CD3.
[0555] I2C-based bispecific single chain antibodies directed at
membrane-proximal target epitopes of human c-MET were designed as
set out in the following Table 7:
TABLE-US-00009 TABLE 7 Formats of I2C-based bispecific single chain
antibodies directed at membrane-proximal target epitopes of human
c-MET SEQ ID Formats of protein constructs (nucl/prot) (N .fwdarw.
C) 512/511 ME86H11HL .times. I2CHL 526/525 ME62A12HL .times. I2CHL
540/539 ME63F2HL .times. I2CHL 554/553 ME62D11HL .times. I2CHL
568/567 ME62C10HL .times. I2CHL 582/581 ME62A4HL .times. I2CHL
[0556] Alternatively further constructs with different domain
arrangements can be generated according to standard protocolls. For
expression in CHO cells the coding sequences of (i) an N-terminal
immunoglobulin heavy chain leader comprising a start codon embedded
within a Kozak consensus sequence and (ii) a C-terminal His6-tag
followed by a stop codon are both attached in frame to the
nucleotide sequence encoding the bispecific single chain antibodies
prior to insertion of the resulting DNA-fragment as obtained by
gene synthesis into the multiple cloning site of the expression
vector pEF-DHFR (Raum et al. Cancer Immunol Immunother 50 (2001)
141-150). A clone with sequence-verified nucleotide sequence is
transfected into DHFR deficient CHO cells for eukaryotic expression
of the construct. Eukaryotic protein expression in DHFR deficient
CHO cells is performed as described by Kaufmann R. J. (1990)
Methods Enzymol. 185, 537-566. Gene amplification of the construct
is induced by increasing concentrations of methotrexate (MTX) to a
final concentration of up to 20 nM MTX.
7.12 Expression and Purification of Bispecific Single Chain
Antibody Molecules Directed at Membrane-Proximal Target Epitopes of
Human c-MET
[0557] Bispecific single chain antibody molecules are expressed in
Chinese hamster ovary cells (CHO). Eukaryotic protein expression in
DHFR deficient CHO cells is performed as described by Kaufmann R.
J. (1990) Methods Enzymol. 185, 537-566. Gene amplification of the
constructs is induced by addition of increasing concentrations of
MTX up to final concentrations of 20 nM MTX. After two passages of
stationary culture cell culture supernatant is collected and used
in the subsequent experiments. To generate supernatant for
purification after two passages of stationary culture the cells are
grown in roller bottles with nucleoside-free HyQ PF CHO liquid soy
medium (with 4.0 mM L-Glutamine with 0.1% Pluronic F-68; HyClone)
for 7 days before harvest. The cells are removed by centrifugation
and the supernatant containing the expressed protein is stored at
-20.degree. C. Alternatively, constructs are transiently expressed
in HEK 293 cells. Transfection is performed with 293fectin reagent
(Invitrogen, #12347-019) according to the manufacturer's protocol.
Furthermore the constructs are alternatively expressed in
transiently transfected DHFR deficient CHO cells using for example
FuGENE.RTM. HD Transfection Reagent (Roche Diagnostics GmbH, Cat.
No. 04709691001) according to the manufacturer's protocol.
[0558] Akta.RTM. Explorer System (GE Health Systems) and
Unicorn.RTM. Software are used for chromatography. Immobilized
metal affinity chromatography ("IMAC") is performed using a
Fractogel EMD Chelate.RTM. (Merck) which is loaded with ZnCl.sub.2
according to the protocol provided by the manufacturer. The column
is equilibrated with buffer A (20 mM sodium phosphate buffer pH
7.2, 0.1 M NaCl) and the cell culture supernatant (500 ml) is
applied to the column (10 ml) at a flow rate of 3 ml/min. The
column is washed with buffer A to remove unbound sample. Bound
protein is eluted using a two step gradient of buffer B (20 mM
sodium phosphate buffer pH 7.2, 0.1 M NaCl, 0.5 M Imidazole)
according to the following procedure:
[0559] Step 1: 20% buffer B in 6 column volumes
[0560] Step 2: 100% buffer B in 6 column volumes
[0561] Eluted protein fractions from step 2 are pooled for further
purification. All chemicals are of research grade and purchased
from Sigma (Deisenhofen) or Merck (Darmstadt).
[0562] Gel filtration chromatography is performed on a HiLoad 16/60
Superdex 200 prep grade column (GE/Amersham) equilibrated with
Equi-buffer (25 mM Citrate, 200 mM Lysine, 5% Glycerol, pH 7.2).
Eluted protein samples (flow rate 1 ml/min) are subjected to
standard SDS-PAGE and Western Blot for detection. Prior to
purification, the column is calibrated for molecular weight
determination (molecular weight marker kit, Sigma MW GF-200).
Protein concentrations are determined using OD280 nm.
[0563] Purified bispecific single chain antibody protein is
analyzed in SDS PAGE under reducing conditions performed with
pre-cast 4-12% Bis Tris gels (Invitrogen). Sample preparation and
application are performed according to the protocol provided by the
manufacturer. The molecular weight is determined with MultiMark
protein standard (Invitrogen). The gel is stained with colloidal
Coomassie (Invitrogen protocol). The purity of the isolated protein
is typically >95% as determined by SDS-PAGE.
[0564] The bispecific single chain antibody has a molecular weight
of about 52 kDa under native conditions as determined by gel
filtration in PBS.
[0565] Western Blot is performed using an Optitran.RTM. BA-S83
membrane and the Invitrogen Blot Module according to the protocol
provided by the manufacturer. The antibody used is directed against
the His Tag (Penta His, Qiagen) and a Goat-anti-mouse Ig labeled
with alkaline phosphatase (AP) (Sigma) is used as second step
reagent, and BCIP/NBT (Sigma) as substrate. A band detected at 52
kD corresponds to purified bispecific single chain antibodies.
7.13 Flow Cytometric Binding Analysis of Bispecific Antibodies
Directed at Membrane-Proximal Target Epitopes of Human c-MET
[0566] In order to test the functionality of bispecific antibody
constructs regarding the capability to bind to CD3 and to
membrane-proximal target epitopes of human c-MET, respectively, a
FACS analysis is performed. For this purpose CHO cells transfected
with human c-MET as described in Example 7.17 and the human CD3
positive T cell leukemia cell line HPB-ALL (DSMZ, Braunschweig,
ACC483) are used. For confirmation of binding to membrane-proximal
target epitopes of human c-MET--in addition--CHO cells expressing
the murine c-MET antigen as described in Example 7.17, CHO cells
expressing the mutated human c-MET antigen with murine
membrane-distal epitopes as described in Example 7.17 and CHO cells
expressing the mutated murine c-MET antigen with human
membrane-distal epitopes as described in Example 7.17 are used.
200.000 cells of the respective cell lines are incubated for 30 min
on ice with 50 .mu.l of cell culture supernatant of transfected
cells expressing the bispecific antibody constructs. The cells are
washed twice in PBS with 2% FCS and binding of the construct is
detected with a murine Penta His antibody (Qiagen; diluted 1:20 in
50 .mu.l PBS with 2% FCS). After washing, bound anti His antibodies
are detected with an Fc gamma-specific antibody (Dianova)
conjugated to phycoerythrin, diluted 1:100 in PBS with 2% FCS.
Supernatant of untransfected cells is used as a negative
control.
[0567] Flow cytometry is performed on a FACS-Calibur apparatus, the
CellQuest software is used to acquire and analyze the data (Becton
Dickinson biosciences, Heidelberg). FACS staining and measuring of
the fluorescence intensity are performed as described in Current
Protocols in Immunology (Coligan, Kruisbeek, Margulies, Shevach and
Strober, Wiley-Interscience, 2002).
[0568] Only those constructs that show bispecific binding to human
CD3 as well as to human c-MET and neither bind to the murine c-MET
antigen nor to the mutated murine c-MET antigen with human
membrane-distal epitopes are selected for further use.
[0569] The bispecific binding of the single chain molecules listed
above was clearly detectable as shown in FIG. 13. In the FACS
analysis all constructs showed binding to human CD3 and human c-MET
compared to the negative control.
[0570] Membrane-proximal target binding of the single chain
molecules listed above was clearly detectable as shown in FIG. 14.
In the FACS analysis all constructs showed binding to the mutated
human c-MET antigen with murine membrane-distal epitopes and did
not show binding to the murine c-MET antigen and did also not show
binding to the mutated murine c-MET antigen with human
membrane-distal epitopes as compared to the negative control.
Expression of the c-MET antigens was confirmed by detection with an
anti-FLAG M2 antibody as described herein. In the FACS analysis
also shown in FIG. 14 CHO cells transfected with the murine c-MET
antigen, the mutated murine c-MET antigen with human
membrane-distal epitopes and the mutated human c-MET antigen with
murine membrane-distal epitopes, respectively, showed comparable
expression of the antigens as detected with the anti-FLAG
antibody.
7.14 Bioactivity of Bispecific Antibodies Directed at
Membrane-Proximal Target Epitopes of Human c-MET
[0571] Bioactivity of generated bispecific single chain antibodies
is analyzed by chromium 51 (.sup.51Cr) release in vitro
cytotoxicity assays using the CHO cells transfected with human
c-MET described in Example 7.17. To confirm that significant
bioactivity is only recruited by binding to membrane-proximal
target epitopes of human c-MET--in addition--CHO cells expressing
murine c-MET and the mutated murine c-MET antigen with human
membrane-distal epitopes, respectively, both as described in
Example 7.17 are used. As effector cells stimulated human CD4/CD56
depleted PBMC are used.
[0572] Stimulated human PBMC are obtained as follows:
[0573] A Petri dish (145 mm diameter, Greiner bio-one GmbH,
Kremsmunster) is coated with a commercially available anti-CD3
specific antibody (e.g. OKT3, Orthoclone) in a final concentration
of 1 .mu.g/ml for 1 hour at 37.degree. C. Unbound protein is
removed by one washing step with PBS. The fresh PBMC are isolated
from peripheral blood (30-50 ml human blood) by Ficoll gradient
centrifugation according to standard protocols. 3-5.times.10.sup.7
PBMC are added to the precoated petri dish in 120 ml of RPMI 1640
with stabilized glutamine/10% FCS/IL-2 20 U/ml (Proleukin, Chiron)
and stimulated for 2 days. On the third day the cells are collected
and washed once with RPMI 1640. IL 2 is added to a final
concentration of 20 U/ml and the cells are cultivated again for one
day in the same cell culture medium as above.
[0574] By depletion of CD4+ T cells and CD56+NK cells according to
standard protocols CD8+ cytotoxic T lymphocytes (CTLs) are
enriched.
[0575] Target cells are washed twice with PBS and labeled with 11.1
MBq .sup.51Cr in a final volume of 100 .mu.l RPMI with 50% FCS for
60 minutes at 37.degree. C. Subsequently the labeled target cells
are washed 3 times with 5 ml RPMI and then used in the cytotoxicity
assay. The assay is performed in a 96 well plate in a total volume
of 250 .mu.l supplemented RPMI (as above) with an E:T ratio of
10:1. Supernatant of cells expressing the bispecific single chain
antibody molecules in a final concentration of 50% and 20 threefold
dilutions thereof are applied. The assay time is 18 hours.
Cytotoxicity is measured as relative values of released chromium in
the supernatant related to the difference of maximum lysis
(addition of Triton-X) and spontaneous lysis (without effector
cells). All measurements are done in quadruplicates. Measurement of
chromium activity in the supernatants is performed with a Wizard
3'' gammacounter (Perkin Elmer Life Sciences GmbH, Koln, Germany).
Analysis of the experimental data is performed with Prism 4 for
Windows (version 4.02, GraphPad Software Inc., San Diego, Calif.,
USA). Sigmoidal dose response curves typically have R.sup.2 values
>0.90 as determined by the software.
[0576] Only those constructs showing potent recruitment of
cytotoxic activity of effector T cells against target cells
positive for c-MET are selected for further use.
[0577] As shown in FIG. 15 all of the generated bispecific
antibodies directed at membrane-proximal target epitopes of human
c-MET demonstrated cytotoxic activity against human c-MET positive
target cells elicited by stimulated human CD4/CD56 depleted PBMC
but did not recruit significant cytotoxic activity against murine
c-MET positive target cells and target cells positive for the
mutated murine c-MET antigen with human membrane-distal epitopes.
Thereby specific recruitment of cytotoxic activity via binding to
membrane-proximal target epitopes of human c-MET was confirmed.
7.15 Generation of CHO Cells Expressing Macaque c-MET
[0578] The cDNA sequence of macaque c-MET is obtained by a set of 5
PCRs on cDNA from macaque monkey Liver prepared according to
standard protocols. The following reaction conditions: 1 cycle at
94.degree. C. for 2 minutes followed by 40 cycles with 94.degree.
C. for 1 minute, 56.degree. C. for 1 minute and 72.degree. C. for 3
minutes followed by a terminal cycle of 72.degree. C. for 3 minutes
and the following primers are used:
TABLE-US-00010 1. forward primer: SEQ ID NO: 396
5'-aggaattcaccatgaaggcccccgctgtgcttgcacc-3' reverse primer: SEQ ID
NO: 397 5'-ctccagaggcatttccatgtagg-3' 2. forward primer: SEQ ID NO:
398 5'-gtccaaagggaaactctagatgc-3' reverse primer: SEQ ID NO: 399
5'-ggagacactggatgggagtccagg-3' 3. forward primer: SEQ ID NO: 400
5'-catcagagggtcgcttcatgcagg-3' reverse primer: SEQ ID NO: 401
5'-gctttggttttcagggggagttgc-3' 4. forward primer: SEQ ID NO: 402
5'-atccaaccaaatcttttattagtggtgg-3' reverse primer: SEQ ID NO: 403
5'-gacttcattgaaatgcacaatcagg-3' 5. forward primer: SEQ ID NO: 404
5'-tgctctaaatccagagctggtcc-3' reverse primer: SEQ ID NO: 405
5'-gtcagataagaaattccttagaatcc-3'
[0579] These PCRs generate five overlapping fragments, which are
isolated and sequenced according to standard protocols using the
PCR primers, and thereby provide a portion of the cDNA sequence
coding macaque c-MET from codon 10 of the leader peptide to the
last codon of the mature protein. To generate a construct for
expression of macaque c-MET a cDNA fragment is obtained by gene
synthesis according to standard protocols (the cDNA and amino acid
sequence of the construct is listed under SEQ ID Nos 406 and 407).
In this construct the coding sequence of macaque c-MET from amino
acid 10 of the leader peptide to the last amino acid of the mature
c-MET protein followed by a stop codon is fused in frame to the
coding sequence of the amino acids 1 to 9 of the leader peptide of
the human c-MET protein. The gene synthesis fragment is also
designed as to contain a Kozak site for eukaryotic expression of
the construct and restriction sites at the beginning and the end of
the fragment containing the cDNA. The introduced restriction sites,
EcoRI at the 5' end and SalI at the 3' end, are utilised in the
following cloning procedures. Internal restriction sites are
removed by silent mutation of the coding sequence in the gene
synthesis fragment. The gene synthesis fragment is cloned via EcoRI
and SalI into a plasmid designated pEF-DHFR (pEF-DHFR is described
in Raum et al. Cancer Immunol Immunother 50 (2001) 141-150)
following standard protocols. The aforementioned procedures are
carried out according to standard protocols (Sambrook, Molecular
Cloning; A Laboratory Manual, 3rd edition, Cold Spring Harbour
Laboratory Press, Cold Spring Harbour, New York (2001)). A clone
with sequence-verified nucleotide sequence is transfected into DHFR
deficient CHO cells for eukaryotic expression of the construct.
Eukaryotic protein expression in DHFR deficient CHO cells is
performed as described by Kaufmann R. J. (1990) Methods Enzymol.
185, 537-566. Gene amplification of the construct is induced by
increasing concentrations of methotrexate (MTX) to a final
concentration of up to 20 nM MTX.
7.16 Flow Cytometric Analysis of Cross-Species Specificity of
Bispecific Antibodies Directed at Membrane-Proximal Target Epitopes
of Human c-MET
[0580] In order to test the cross-species specificity of bispecific
antibodies directed at membrane-proximal target epitopes of human
c-MET the capability of the constructs to bind to macaque c-MET and
macaque CD3, respectively, is investigated by FACS analysis. For
this purpose the macaque c-MET transfected CHO cells as described
in example 7.17 and the macaque T cell line 4119LnPx (kindly
provided by Prof Fickenscher, Hygiene Institute, Virology,
Erlangen-Nuernberg; published in Knappe A, et al., and Fickenscher
H., Blood 2000, 95, 3256-61) are used. 200.000 cells of the
respective cell lines are incubated for 30 min on ice with with 50
.mu.l of cell culture supernatant of transfected cells expressing
the cross-species specific bispecific antibody constructs. The
cells are washed twice in PBS with 2% FCS and binding of the
construct is detected with a murine Penta His antibody (Qiagen;
diluted 1:20 in 50 .mu.l PBS with 2% FCS). After washing, bound
anti His antibodies are detected with an Fc gamma-specific antibody
(Dianova) conjugated to phycoerythrin, diluted 1:100 in PBS with 2%
FCS. Supernatant of untransfected cells is used as a negative
control. Flow cytometry is performed on a FACS-Calibur apparatus,
the CellQuest software is used to acquire and analyze the data
(Becton Dickinson biosciences, Heidelberg). FACS staining and
measuring of the fluorescence intensity are performed as described
in Current Protocols in Immunology (Coligan, Kruisbeek, Margulies,
Shevach and Strober, Wiley-Interscience, 2002).
[0581] The cross-species specific binding of the single chain
molecules listed above was clearly detectable as shown in FIG. 13.
In the FACS analysis all constructs showed binding to macaque CD3
and macaque c-MET compared to the negative control.
7.17 Generation of CHO Cells with Enhanced Expression of
Extracellular Domains of Human c-MET, Macaque c-MET, Murine c-MET,
Mutated Murine c-MET with Human Membrane-Distal Epitopes and
Mutated Human c-MET with Murine Membrane-Distal Epitopes,
Respectively
[0582] The modified coding sequences of human c-MET, macaque c-MET,
murine c-MET, mutated murine c-MET with human membrane-distal
epitopes and mutated human c-MET with murine membrane-distal
epitopes as described above are used for the construction of
artificial cDNA sequences encoding fusion proteins of the
extracellular domains of human c-MET, macaque c-MET, murine c-MET,
mutated murine c-MET with human membrane-distal epitopes and
mutated human c-MET with murine membrane-distal epitopes,
respectively, with a truncated variant of human EpCAM. To generate
constructs for expression of these c-MET fusion proteins cDNA
fragments are obtained by gene synthesis according to standard
protocols (the cDNA and amino acid sequences of the constructs are
listed under SEQ ID Nos 489 and 490 for human c-MET, 491 and 492
for macaque c-MET, 493 and 494 for murine c-MET, 495 and 496 for
mutated murine c-MET with human membrane-distal epitopes and 497
and 498 for mutated human c-MET with murine membrane-distal
epitopes). The gene synthesis fragments are designed as to contain
first a Kozak site for eukaryotic expression of the construct,
followed by the coding sequence of a 19 amino acid immunoglobulin
leader peptide, followed in frame by the coding sequence of a FLAG
tag (only in the case of the murine and the mutated human and
mutated murine constructs), followed in frame by the coding
sequence of the extracellular domains of human c-MET, macaque
c-MET, murine c-MET, mutated murine c-MET with human
membrane-distal epitopes and mutated human c-MET with murine
membrane-distal epitopes, respectively, followed in frame by the
coding sequence of an artificial
Ser.sub.1-Gly.sub.4-Ser.sub.1-Gly.sub.1-linker, followed in frame
by the coding sequence of the transmembrane domain and
intracellular domain of human EpCAM (as published in GenBank;
Accession number NM_002354; amino acids 266 to 314 [as counted from
the start codon] except for a point mutation at position 279 with
isoleucine instead of valine) and a stop codon. The gene synthesis
fragments are also designed as to introduce restriction sites at
the beginning and at the end of the fragment. The introduced
restriction sites, EcoRI at the 5' end and SalI at the 3' end, are
utilized in the following cloning procedures. The gene synthesis
fragments are cloned via EcoRI and SalI into a plasmid designated
pEF-DHFR (pEF-DHFR is described in Raum et al. Cancer Immunol
Immunother 50 (2001) 141-150) following standard protocols. Clones
with sequence-verified nucleotide sequence are transfected into
DHFR deficient CHO cells for eukaryotic expression of the
constructs. Eukaryotic protein expression in DHFR deficient CHO
cells is performed as described by Kaufmann R. J. (1990) Methods
Enzymol. 185, 537-566. Gene amplification of the constructs is
induced by increasing concentrations of methotrexate (MTX) to a
final concentration of up to 20 nM MTX.
8. Generation of Bispecific Single Chain Antibodies Directed at
Membrane-Proximal Target Epitopes of Human Endosialin
8.1 Generation of CHO Cells Expressing Human Endosialin
[0583] The coding sequence of human Endosialin as published in
GenBank (Accession number NM_020404) is obtained by gene synthesis
according to standard protocols. The gene synthesis fragment is
designed as to contain first a Kozak site for eukaryotic expression
of the construct followed by the coding sequence of the human
Endosialin protein, followed in frame by the coding sequence of a
Flag tag and a stop codon (the cDNA and amino acid sequence of the
construct is listed under SEQ ID Nos 408 and 409). The gene
synthesis fragment is also designed as to introduce restriction
sites at the beginning and at the end of the fragment. The
introduced restriction sites, EcoRI at the 5' end and XbaI at the
3' end, are utilized in the following cloning procedures. The gene
synthesis fragment is cloned via EcoRI and XbaI into a plasmid
designated pEF-DHFR (pEF-DHFR is described in Raum et al. Cancer
Immunol Immunother 50 (2001) 141-150) following standard protocols.
The aforementioned procedures are carried out according to standard
protocols (Sambrook, Molecular Cloning; A Laboratory Manual, 3rd
edition, Cold Spring Harbour Laboratory Press, Cold Spring Harbour,
New York (2001)). A clone with sequence-verified nucleotide
sequence is transfected into DHFR deficient CHO cells for
eukaryotic expression of the construct. Eukaryotic protein
expression in DHFR deficient CHO cells is performed as described by
Kaufmann R. J. (1990) Methods Enzymol. 185, 537-566. Gene
amplification of the construct is induced by increasing
concentrations of methotrexate (MTX) to a final concentration of up
to 20 nM MTX.
8.2 Generation of a Soluble Human Endosialin Fusion Protein
[0584] The coding sequence of human Endosialin as described in
Example 8.1 is used for the construction of an artificial cDNA
sequence encoding a soluble fusion protein of human Endosialin and
murine IgG1 Fc. To generate a construct for expression of the
soluble human Endosialin fusion protein .alpha. cDNA fragment is
obtained by gene synthesis according to standard protocols (the
cDNA and amino acid sequence of the construct is listed under SEQ
ID Nos 410 and 411). The gene synthesis fragment is designed as to
contain first a Kozak site for eukaryotic expression of the
construct followed by the coding sequence of the human Endosialin
protein from amino acid 1 to 685 corresponding to the signal
peptide and extracellular domains of human Endosialin, followed in
frame by the coding sequence of an artificial
Thr.sub.1-Gly.sub.4-Ser.sub.1-linker, followed in frame by the
coding sequence of the hinge region and Fc gamma portion of murine
IgG1, followed in frame by the coding sequence of a 6 histidine tag
and a stop codon. The gene synthesis fragment is also designed as
to introduce restriction sites at the beginning and at the end of
the fragment. The introduced restriction sites, EcoRI at the 5' end
and XbaI at the 3' end, are utilized in the following cloning
procedures. The gene synthesis fragment is cloned via EcoRI and
XbaI into a plasmid designated pEF-DHFR (pEF-DHFR is described in
Raum et al. Cancer Immunol Immunother 50 (2001) 141-150) following
standard protocols. The aforementioned procedures are all carried
out according to standard protocols (Sambrook, Molecular Cloning; A
Laboratory Manual, 3rd edition, Cold Spring Harbour Laboratory
Press, Cold Spring Harbour, New York (2001)). A clone with
sequence-verified nucleotide sequence is transfected into DHFR
deficient CHO cells for eukaryotic expression of the construct.
Eukaryotic protein expression in DHFR deficient CHO cells is
performed as described by Kaufmann R. J. (1990) Methods Enzymol.
185, 537-566. Gene amplification of the construct is induced by
increasing concentrations of methotrexate (MTX) to a final
concentration of up to 20 nM MTX. After two passages of stationary
culture the cells are grown in roller bottles with nucleoside-free
HyQ PF CHO liquid soy medium (with 4.0 mM L-Glutamine with 0.1%
Pluronic F--68; HyClone) for 7 days before harvest. The cells are
removed by centrifugation and the supernatant containing the
expressed protein is stored at -20.degree. C. Alternatively a clone
of the expression plasmid with sequence-verified nucleotide
sequence is used for transfection and protein expression in the
FreeStyle 293 Expression System (Invitrogen GmbH, Karlsruhe,
Germany) according to the manufacturer's protocol. Supernatant
containing the expressed protein is obtained, cells are removed by
centrifugation and the supernatant is stored at -20.degree. C.
[0585] For purification of the soluble human Endosialin fusion
protein .alpha. goat anti-mouse Fc affinity column is prepared
according to standard protocols using a commercially available
affinity purified goat anti-mouse IgG Fc fragment specific antibody
with minimal cross-reaction to human, bovine and horse serum
proteins (Jackson ImmunoResearch Europe Ltd.). Using this affinity
column the fusion protein is isolated out of cell culture
supernatant on an Akta Explorer System (GE Amersham) and eluted by
citric acid. The eluate is neutralized and concentrated.
8.3 Generation of CHO Cells Expressing the Murine Endosialin
Antigen
[0586] The sequence of murine Endosialin (NM_054042 Mus musculus
Endosialin antigen, endosialin (Cd248), mRNA; National Center for
Biotechnology Information, http://www.ncbi.nlm.nih.gov/entrez) is
used to obtain a synthetic cDNA molecule by gene synthesis
according to standard protocols. The gene synthesis fragment is
designed as to contain the coding sequence of an immunoglobulin
heavy chain leader comprising a start codon embedded within a Kozak
consensus sequence, followed in frame by the coding sequence of a
FLAG tag, followed in frame by the complete coding sequence of
mature murine endosialin (the cDNA and amino acid sequence of the
construct is listed under SEQ ID Nos 412 and 413). The gene
synthesis fragment is also designed as to introduce restriction
sites at the 5' end (EcoRI) and at the 3' end (Sal I) of the cDNA
fragment for cloning into the mammalian cell expression vector
pEF-DHFR (pEF-DHFR is described in Raum et al. Cancer Immunol
Immunother 50 (2001) 141-150). The aforementioned procedures are
carried out according to standard protocols (Sambrook, Molecular
Cloning; A Laboratory Manual, 3rd edition, Cold Spring Harbour
Laboratory Press, Cold Spring Harbour, New York (2001)). A clone
with sequence-verified nucleotide sequence is transfected into DHFR
deficient CHO cells for eukaryotic expression of the construct.
Eukaryotic protein expression in DHFR deficient CHO cells is
performed as described by Kaufmann R. J. (1990) Methods Enzymol.
185, 537-566. Gene amplification for increased antigen expression
is induced by increasing concentrations of methotrexate (MTX) to a
final concentration of up to 20 nM MTX.
8.4 Generation of CHO Cells Expressing a Mutated Human Endosialin
Antigen with Murine Membrane-Distal Epitopes
[0587] The coding sequence of a mutated human Endosialin antigen
with murine membrane-distal epitopes is obtained by gene synthesis
according to standard protocols. The gene synthesis fragment is
designed as to contain the coding sequence of an immunoglobulin
heavy chain leader comprising a start codon embedded within a Kozak
consensus sequence, followed in frame by the coding sequence of a
FLAG tag, followed in frame by the coding sequence of the C-type
lectin domain of mature murine endosialin followed in frame by
human endosialin from the Sushi/SCR/CCP domain to the stop codon
(the cDNA and amino acid sequence of the construct is listed under
SEQ ID Nos 414 and 415). The gene synthesis fragment is also
designed as to introduce restriction sites at the 5' end (EcoRI)
and at the 3' end (Sal I) of the cDNA fragment for cloning into the
mammalian cell expression vector pEF-DHFR (pEF-DHFR is described in
Raum et al. Cancer Immunol Immunother 50 (2001) 141-150). The
aforementioned procedures are carried out according to standard
protocols (Sambrook, Molecular Cloning; A Laboratory Manual, 3rd
edition, Cold Spring Harbour Laboratory Press, Cold Spring Harbour,
New York (2001)). A clone with sequence-verified nucleotide
sequence is transfected into DHFR deficient CHO cells for
eukaryotic expression of the construct. Eukaryotic protein
expression in DHFR deficient CHO cells is performed as described by
Kaufmann R. J. (1990) Methods Enzymol. 185, 537-566. Gene
amplification for increased antigen expression is induced by
increasing concentrations of methotrexate (MTX) to a final
concentration of up to 20 nM MTX.
8.5 Generation of CHO Cells Expressing a Mutated Murine Endosialin
Antigen with Human Membrane-Distal Epitopes
[0588] The coding sequence of a mutated murine Endosialin antigen
with human membrane-distal epitopes is obtained by gene synthesis
according to standard protocols. The gene synthesis fragment is
designed as to contain the coding sequence of an immunoglobulin
heavy chain leader comprising a start codon embedded within a Kozak
consensus sequence, followed in frame by the coding sequence of a
FLAG tag, followed in frame by the coding sequence of the C-type
lectin domain of mature human endosialin followed in frame by
murine endosialin from the Sushi/SCR/CCP domain to the stop codon
(the cDNA and amino acid sequence of the construct is listed under
SEQ ID Nos 416 and 417). The gene synthesis fragment is also
designed as to introduce restriction sites at the 5' end (EcoRI)
and at the 3' end (Sal I) of the cDNA fragment for cloning into the
mammalian cell expression vector pEF-DHFR (pEF-DHFR is described in
Raum et al. Cancer Immunol Immunother 50 (2001) 141-150). Internal
restriction sites are removed by silent mutation of the coding
sequence in the gene synthesis fragment. The aforementioned
procedures are carried out according to standard protocols
(Sambrook, Molecular Cloning; A Laboratory Manual, 3rd edition,
Cold Spring Harbour Laboratory Press, Cold Spring Harbour, New York
(2001)). A clone with sequence-verified nucleotide sequence is
transfected into DHFR deficient CHO cells for eukaryotic expression
of the construct. Eukaryotic protein expression in DHFR deficient
CHO cells is performed as described by Kaufmann R. J. (1990)
Methods Enzymol. 185, 537-566. Gene amplification for increased
antigen expression is induced by increasing concentrations of
methotrexate (MTX) to a final concentration of up to 20 nM MTX.
8.6 Immunization of Mice Using a Soluble Human Endosialin Fusion
Protein
[0589] Twelve weeks old F1 mice from BALB/c.times.C57BL/6 crossings
are immunized with the soluble human Endosialin fusion protein as
described in Example 8.2. To this end for each animal 40 .mu.g of
the soluble human Endosialin fusion protein are mixed with 10 nmol
of a thioate-modified CpG-Oligonucleotide
(5'-tccatgacgttcctgatgct-3') in 300 .mu.l PBS and are injected
intraperitoneally. Mice receive booster immunizations after 21, 42
and optionally 63 days in the same way. Ten days after the first
booster immunization, blood samples are taken and antibody serum
titers against human Endosialin are tested by flow cytometry
according to standard protocols. To this end 200.000 cells of the
human Endosialin transfected CHO cells as described in Example 8.1
are incubated for 30 min on ice with 50 .mu.l of serum of the
immunized animals diluted 1:1000 in PBS with 2% FCS. The cells are
washed twice in PBS with 2% FCS and binding of serum antibodies is
detected with an mouse Fc gamma-specific antibody (Dianova)
conjugated to phycoerythrin, diluted 1:100 in PBS with 2% FCS.
Serum of the animals obtained prior to immunization is used as a
negative control.
[0590] Flow cytometry is performed on a FACS-Calibur apparatus, the
CellQuest software is used to acquire and analyze the data (Becton
Dickinson biosciences, Heidelberg). FACS staining and measuring of
the fluorescence intensity are performed as described in Current
Protocols in Immunology (Coligan, Kruisbeek, Margulies, Shevach and
Strober, Wiley-Interscience, 2002).
[0591] Animals demonstrating significant serum reactivity against
human Endosialin as determined by the FACS analysis are used in the
subsequent experiment.
8.7 Generation of an Immune Murine Antibody scFv Library:
Construction of a Combinatorial Antibody Library and Phage
Display
[0592] Three days after the last booster immunization spleen cells
of reactive animals are harvested for the preparation of total RNA
according to standard protocols. A library of murine immunoglobulin
(Ig) light chain (kappa) variable region (VK) and Ig heavy chain
variable region (VH) DNA-fragments is constructed by RT-PCR on
murine spleen RNA using VK- and VH specific primers. cDNA is
synthesized according to standard protocols, see example 2.7.
[0593] 450 ng of the kappa light chain fragments (SacI-SpeI
digested) are ligated with 1400 ng of the phagemid pComb3H5Bhis
(SacI-SpeI digested; large fragment). The resulting combinatorial
antibody library is then transformed into 300 .mu.l of
electrocompetent Escherichia coli XL1 Blue cells by electroporation
(2.5 kV, 0.2 cm gap cuvette, 25 .mu.FD, 200 Ohm, Biorad
gene-pulser) resulting in a library size of more than 10.sup.7
independent clones. After one hour of phenotype expression,
positive transformants are selected for carbenicillin resistance
encoded by the pComb3H5BHis vector in 100 ml of liquid super broth
(SB)-culture over night. Cells are then harvested by centrifugation
and plasmid preparation is carried out using a commercially
available plasmid preparation kit (Qiagen).
[0594] 2800 ng of this plasmid-DNA containing the VK-library
(XhoI-BstElI digested; large fragment) are ligated with 900 ng of
the heavy chain V-fragments (XhoI-BstElI digested) and again
transformed into two 300 .mu.l aliquots of electrocompetent E. coli
XL1 Blue cells by electroporation (2.5 kV, 0.2 cm gap cuvette, 25
.mu.FD, 200 Ohm) resulting in a total VH-VK scFv (single chain
variable fragment) library size of more than 10.sup.7 independent
clones.
[0595] After phenotype expression and slow adaptation to
carbenicillin, the E. coli cells containing the antibody library
are transferred into SB-Carbenicillin (SB with 50 .mu.g/mL
carbenicillin) selection medium. The E. coli cells containing the
antibody library are then infected with an infectious dose of
10.sup.12 particles of helper phage VCSM13 resulting in the
production and secretion of filamentous M13 phage, wherein each
phage particle contains single stranded pComb3H5BHis-DNA encoding a
murine scFv-fragment and displays the corresponding scFv-protein as
a translational fusion to phage coat protein III. This pool of
phages displaying the antibody library is later used for the
selection of antigen binding entities.
8.8 Phage Display Based Selection of Membrane-Proximal Target
Binders on CHO Cells Expressing the Mutated Human Endosialin
Antigen with Murine Membrane-Distal Epitopes
[0596] The phage library carrying the cloned scFv-repertoire is
harvested from the respective culture supernatant by PEG8000/NaCl
precipitation and centrifugation. Approximately 10.sup.11 to
10.sup.12 scFv phage particles are resuspended in 0.4 ml of
PBS/0.1% BSA and incubated with 10.sup.5 to 10.sup.7 CHO cells
expressing the mutated human Endosialin antigen with murine
membrane-distal epitopes as described in example 8.4 for 1 hour on
ice under slow agitation. These CHO cells are grown beforehand,
harvested by centrifugation, washed in PBS and resuspended in
PBS/1% FCS (containing Na Azide). scFv phage which do not
specifically bind to the CHO cells are eliminated by up to five
washing steps with PBS/1% FCS (containing Na Azide). After washing,
binding entities are eluted from the cells by resuspending the
cells in HCl-glycine pH 2.2 (10 min incubation with subsequent
vortexing) and after neutralization with 2 M Tris pH 12, the eluate
is used for infection of a fresh uninfected E. coli XL1 Blue
culture (OD600>0.5). The E. coli culture containing E. coli
cells successfully transduced with a phagemid copy, encoding a
murine scFv-fragment, are again selected for carbenicillin
resistance and subsequently infected with VCMS 13 helper phage to
start the second round of antibody display and in vitro selection.
Typically a total of 4 to 5 rounds of selections are carried
out.
8.9 Screening for Membrane-Proximal Target Binders on CHO Cells
Expressing the Human Endosialin Antigen, the Murine Endosialin
Antigen and the Mutated Murine Endosialin Antigen with Human
Membrane-Distal Epitopes
[0597] Plasmid DNA corresponding to 4 and 5 rounds of panning is
isolated from E. coli cultures after selection. For the production
of soluble scFv-protein, VH-VL-DNA fragments are excised from the
plasmids (XhoI-SpeI). These fragments are cloned via the same
restriction sites in the plasmid pComb3H5BFlag/His differing from
the original pComb3H5BHis in that the expression construct (e.g.
scFv) includes a Flag-tag (TGDYKDDDDK) between the scFv and the
His6-tag and the additional phage proteins are deleted. After
ligation, each pool (different rounds of panning) of plasmid DNA is
transformed into 100 .mu.l heat shock competent E. coli TG1 or XLI
blue and plated onto carbenicillin LB-agar. Single colonies are
picked into 100 .mu.l of LB carb (LB with 50 .mu.g/ml
carbenicillin).
[0598] After induction with 1 mM IPTG E. coli transformed with
pComb3H5BFlag/His containing a VL- and VH-segment produce soluble
scFv in sufficient amounts. Due to a suitable signal sequence, the
scFv is exported into the periplasma where it folds into a
functional conformation.
[0599] Single E. coli bacterial colonies from the transformation
plates are picked for periplasmic small scale preparations and
grown in SB-medium (e.g. 10 ml) supplemented with 20 mM MgCl.sub.2
and carbenicillin 50 .mu.g/ml (and re-dissolved in PBS (e.g. 1 ml)
after harvesting. A temperature shock is applied by four rounds of
freezing at -70.degree. C. and thawing at 37.degree. C. whereby the
outer membrane of the bacteria is destroyed and the soluble
periplasmic proteins including the scFvs are released into the
supernatant. After elimination of intact cells and cell-debris by
centrifugation, the supernatant containing the murine anti-human
Endosialin-scFvs is collected and used for further examination.
[0600] Screening of the isolated scFvs for membrane-proximal target
binders is performed by flow cytometry on CHO cells expressing the
human Endosialin antigen as described in Example 8.1, the murine
Endosialin antigen as described in Example 8.3 and the mutated
murine Endosialin antigen with human membrane-distal epitopes as
described in Example 8.5.
[0601] For flow cytometry 2.5.times.10.sup.5 cells of the
respective cell lines are incubated with 50 .mu.l supernatant. The
binding of the constructs is detected with an anti-His antibody
(Penta-His Antibody, BSA free, Qiagen GmbH, Hilden, FRG) at 2
.mu.g/ml in 50 .mu.l PBS with 2% FCS. As a second step reagent a
R-Phycoerythrin-conjugated affinity purified F(ab')2 fragment, goat
anti-mouse IgG (Fc-gamma fragment specific), diluted 1:100 in 50
.mu.l PBS with 2% FCS (Dianova, Hamburg, FRG) is used. The samples
are measured on a FACSscan (BD biosciences, Heidelberg, FRG).
[0602] Only constructs which show binding to CHO cells expressing
the human Endosialin antigen and do not show binding to CHO cells
expressing the murine Endosialin antigen and also do not show
binding to CHO cells expressing the mutated murine Endosialin
antigen with human membrane-distal epitopes are selected for
further use.
8.10 Generation of Human/Humanized Equivalents of Non-Human scFvs
to Membrane-Proximal Target Epitopes of Human Endosialin
[0603] The VH region of a murine anti-Endosialin scFv to a
membrane-proximal target epitope of human Endosialin is aligned
against human antibody germline amino acid sequences. The human
antibody germline VH sequence is chosen which has the closest
homology to the non-human VH and a direct alignment of the two
amino acid sequences is performed. There are a number of framework
residues of the non-human VH that differ from the human VH
framework regions ("different framework positions"). Some of these
residues may contribute to the binding and activity of the antibody
to its target.
[0604] To construct a library that contains the murine CDRs and at
every framework position that differs from the chosen human VH
sequence both possible residues (the human and the maternal murine
amino acid residue), degenerated oligonucleotides are synthesized.
These oligonucleotides incorporate at the differing positions the
human residue with a probability of 75% and the murine residue with
a probability of 25%. For one human VH e.g. six of these
oligonucleotides have to be synthesized that overlap in a terminal
stretch of approximately 20 nucleotides. To this end every second
primer is an antisense primer. Restriction sites within the
oligonucleotides needed for later cloning are deleted.
[0605] These primers may have a length of 60 to 90 nucleotides,
depending on the number of primers that are needed to span over the
whole V sequence.
[0606] These e.g. six primers are mixed in equal amounts (e.g. 1
.mu.l of each primer (primer stocks 20 to 100 .mu.M) to a 20 .mu.l
PCR reaction) and added to a PCR mix consisting of PCR buffer,
nucleotides and Taq polymerase. This mix is incubated at 94.degree.
C. for 3 minutes, 65.degree. C. for 1 minute, 62.degree. C. for 1
minute, 59.degree. C. for 1 minute, 56.degree. C. for 1 minute,
52.degree. C. for 1 minute, 50.degree. C. for 1 minute and at
72.degree. C. for 10 minutes in a PCR cycler. Subsequently the
product is run in an agarose gel electrophoresis and the product of
a size from 200 to 400 base pairs isolated from the gel according
to standard methods.
[0607] This PCR product is then used as a template for a standard
PCR reaction using primers that incorporate suitable N-terminal and
C-terminal cloning restriction sites. The DNA fragment of the
correct size (for a VH approximately 350 nucleotides) is isolated
by agarose gel electrophoresis according to standard methods. In
this way sufficient VH DNA fragment is amplified. This VH fragment
is now a pool of VH fragments that have each one a different amount
of human and murine residues at the respective differing framework
positions (pool of humanized VH). The same procedure is performed
for the VL region of the murine anti-Endosialin scFv to a
membrane-proximal target epitope of human Endosialin (pool of
humanized VL).
[0608] The pool of humanized VH is then combined with the pool of
humanized VL in the phage display vector pComb3H5Bhis to form a
library of functional scFvs from which--after display on
filamentous phage--anti-Endosialin binders to membrane-proximal
target epitopes of human Endosialin are selected, screened,
identified and confirmed as described above for the parental
non-human (murine) anti-Endosialin scFv. Single clones are then
analyzed for favorable properties and amino acid sequence. Those
scFvs, which are closest in amino acid sequence homology to human
germline V-segments, are preferred.
[0609] Human/humanized anti-Endosialin scFvs to membrane-proximal
target epitopes of human Endosialin are converted into recombinant
bispecific single chain antibodies and further characterized as
follows.
8.11 Generation of I2C-Based Bispecific Single Chain Antibodies
Directed at Membrane-Proximal Target Epitopes of Human
Endosialin
[0610] Anti-Endosialin scFvs to membrane-proximal target epitopes
of human Endosialin with favorable properties and amino acid
sequence are converted into recombinant bispecific single chain
antibodies by joining them via a Gly.sub.4Ser.sub.1-linker with the
CD3 specific scFv I2C (SEQ ID NO: 185) to result in constructs with
the domain arrangement
VH.sub.Endosialin-(Gly.sub.4Ser.sub.1).sub.3-VL.sub.Endosialin-Ser.sub.1
Gly.sub.4Ser.sub.1-VH.sub.CD3-(Gly.sub.4Ser.sub.1).sub.3-VL.sub.CD3.
Alternatively further constructs with different domain arrangements
can be generated according to standard protocolls. For expression
in CHO cells the coding sequences of (i) an N-terminal
immunoglobulin heavy chain leader comprising a start codon embedded
within a Kozak consensus sequence and (ii) a C-terminal His6-tag
followed by a stop codon are both attached in frame to the
nucleotide sequence encoding the bispecific single chain antibodies
prior to insertion of the resulting DNA-fragment as obtained by
gene synthesis into the multiple cloning site of the expression
vector pEF-DHFR (Raum et al. Cancer Immunol Immunother 50 (2001)
141-150). A clone with sequence-verified nucleotide sequence is
transfected into DHFR deficient CHO cells for eukaryotic expression
of the construct. Eukaryotic protein expression in DHFR deficient
CHO cells is performed as described by Kaufmann R. J. (1990)
Methods Enzymol. 185, 537-566. Gene amplification of the construct
is induced by increasing concentrations of methotrexate (MTX) to a
final concentration of up to 20 nM MTX.
8.12 Expression and Purification of Bispecific Single Chain
Antibody Molecules Directed at Membrane-Proximal Target Epitopes of
Human Endosialin
[0611] Bispecific single chain antibody molecules are expressed in
Chinese hamster ovary cells (CHO). Eukaryotic protein expression in
DHFR deficient CHO cells is performed as described by Kaufmann R.
J. (1990) Methods Enzymol. 185, 537-566. Gene amplification of the
constructs is induced by addition of increasing concentrations of
MTX up to final concentrations of 20 nM MTX. After two passages of
stationary culture cell culture supernatant is collected and used
in the subsequent experiments. To generate supernatant for
purification after two passages of stationary culture the cells are
grown in roller bottles with nucleoside-free HyQ PF CHO liquid soy
medium (with 4.0 mM L-Glutamine with 0.1% Pluronic F-68; HyClone)
for 7 days before harvest. The cells are removed by centrifugation
and the supernatant containing the expressed protein is stored at
-20.degree. C. Alternatively, constructs are transiently expressed
in HEK 293 cells. Transfection is performed with 293fectin reagent
(Invitrogen, #12347-019) according to the manufacturer's protocol.
Furthermore the constructs are alternatively expressed in
transiently transfected DHFR deficient CHO cells using for example
FuGENE.RTM. HD Transfection Reagent (Roche Diagnostics GmbH, Cat.
No. 04709691001) according to the manufacturer's protocol.
[0612] Akta.RTM. Explorer System (GE Health Systems) and
Unicorn.RTM. Software are used for chromatography. Immobilized
metal affinity chromatography ("IMAC") is performed using a
Fractogel EMD Chelate.RTM. (Merck) which is loaded with ZnCl.sub.2
according to the protocol provided by the manufacturer. The column
is equilibrated with buffer A (20 mM sodium phosphate buffer pH
7.2, 0.1 M NaCl) and the cell culture supernatant (500 ml) is
applied to the column (10 ml) at a flow rate of 3 ml/min. The
column is washed with buffer A to remove unbound sample. Bound
protein is eluted using a two step gradient of buffer B (20 mM
sodium phosphate buffer pH 7.2, 0.1 M NaCl, 0.5 M Imidazole)
according to the following procedure:
[0613] Step 1: 20% buffer B in 6 column volumes
[0614] Step 2: 100% buffer B in 6 column volumes
[0615] Eluted protein fractions from step 2 are pooled for further
purification. All chemicals are of research grade and purchased
from Sigma (Deisenhofen) or Merck (Darmstadt).
[0616] Gel filtration chromatography is performed on a HiLoad 16/60
Superdex 200 prep grade column (GE/Amersham) equilibrated with
Equi-buffer (25 mM Citrate, 200 mM Lysine, 5% Glycerol, pH 7.2).
Eluted protein samples (flow rate 1 ml/min) are subjected to
standard SDS-PAGE and Western Blot for detection. Prior to
purification, the column is calibrated for molecular weight
determination (molecular weight marker kit, Sigma MW GF-200).
Protein concentrations are determined using OD280 nm.
[0617] Purified bispecific single chain antibody protein is
analyzed in SDS PAGE under reducing conditions performed with
pre-cast 4-12% Bis Tris gels (Invitrogen). Sample preparation and
application are performed according to the protocol provided by the
manufacturer. The molecular weight is determined with MultiMark
protein standard (Invitrogen). The gel is stained with colloidal
Coomassie (Invitrogen protocol). The purity of the isolated protein
is typically >95% as determined by SDS-PAGE. The bispecific
single chain antibody has a molecular weight of about 52 kDa under
native conditions as determined by gel filtration in PBS.
[0618] Western Blot is performed using an Optitran.RTM. BA-S83
membrane and the Invitrogen Blot Module according to the protocol
provided by the manufacturer. The antibody used is directed against
the His Tag (Penta His, Qiagen) and a Goat-anti-mouse Ig labeled
with alkaline phosphatase (AP) (Sigma) is used as second step
reagent, and BCIP/NBT (Sigma) as substrate. A band detected at 52
kD corresponds to purified bispecific single chain antibodies.
8.13 Flow Cytometric Binding Analysis of Bispecific Antibodies
Directed at Membrane-Proximal Target Epitopes of Human
Endosialin
[0619] In order to test the functionality of bispecific antibody
constructs regarding the capability to bind to CD3 and to
membrane-proximal target epitopes of human Endosialin,
respectively, a FACS analysis is performed. For this purpose CHO
cells transfected with human Endosialin as described in Example 8.1
and the human CD3 positive T cell leukemia cell line HPB-ALL (DSMZ,
Braunschweig, ACC483) are used. For confirmation of binding to
membrane-proximal target epitopes of human Endosialin--in
addition--CHO cells expressing the murine Endosialin antigen as
described in Example 8.3 and CHO cells expressing the mutated
murine Endosialin antigen with human membrane-distal epitopes as
described in Example 8.5 are used. 200.000 cells of the respective
cell lines are incubated for 30 min on ice with 50 .mu.l of cell
culture supernatant of transfected cells expressing the bispecific
antibody constructs. The cells are washed twice in PBS with 2% FCS
and binding of the construct is detected with a murine Penta His
antibody (Qiagen; diluted 1:20 in 50 .mu.l PBS with 2% FCS). After
washing, bound anti His antibodies are detected with an Fc
gamma-specific antibody (Dianova) conjugated to phycoerythrin,
diluted 1:100 in PBS with 2% FCS. Supernatant of untransfected
cells is used as a negative control. Flow cytometry is performed on
a FACS-Calibur apparatus, the CellQuest software is used to acquire
and analyze the data (Becton Dickinson biosciences, Heidelberg).
FACS staining and measuring of the fluorescence intensity are
performed as described in Current Protocols in Immunology (Coligan,
Kruisbeek, Margulies, Shevach and Strober, Wiley-Interscience,
2002).
[0620] Only those constructs that show bispecific binding to human
CD3 as well as to human Endosialin and neither bind to the murine
Endosialin antigen nor to the mutated murine Endosialin antigen
with human membrane-distal epitopes are selected for further
use.
8.14 Bioactivity of Bispecific Antibodies Directed at
Membrane-Proximal Target Epitopes of Human Endosialin
[0621] Bioactivity of generated bispecific single chain antibodies
is analyzed by chromium 51 (.sup.51Cr) release in vitro
cytotoxicity assays using the CHO cells transfected with human
Endosialin described in Example 8.1. As effector cells stimulated
human CD4/CD56 depleted PBMC are used.
[0622] Stimulated human PBMC are obtained as follows:
[0623] A Petri dish (145 mm diameter, Greiner bio-one GmbH,
Kremsmunster) is coated with a commercially available anti-CD3
specific antibody (e.g. OKT3, Orthoclone) in a final concentration
of 1 .mu.g/ml for 1 hour at 37.degree. C. Unbound protein is
removed by one washing step with PBS. The fresh PBMC are isolated
from peripheral blood (30-50 ml human blood) by Ficoll gradient
centrifugation according to standard protocols. 3-5.times.10.sup.7
PBMC are added to the precoated petri dish in 120 ml of RPMI 1640
with stabilized glutamine/10% FCS/IL-2 20 U/ml (Proleukin, Chiron)
and stimulated for 2 days. On the third day the cells are collected
and washed once with RPMI 1640. IL 2 is added to a final
concentration of 20 U/ml and the cells are cultivated again for one
day in the same cell culture medium as above.
[0624] By depletion of CD4+ T cells and CD56+NK cells according to
standard protocols CD8+ cytotoxic T lymphocytes (CTLs) are
enriched.
[0625] Target cells are washed twice with PBS and labeled with 11.1
MBq .sup.51Cr in a final volume of 100 .mu.l RPMI with 50% FCS for
60 minutes at 37.degree. C. Subsequently the labeled target cells
are washed 3 times with 5 ml RPMI and then used in the cytotoxicity
assay. The assay is performed in a 96 well plate in a total volume
of 250 .mu.l supplemented RPMI (as above) with an E:T ratio of
10:1. 1 .mu.g/ml of purified bispecific single chain antibody
molecule and 20 threefold dilutions thereof are applied. The assay
time is 18 hours. Cytotoxicity is measured as relative values of
released chromium in the supernatant related to the difference of
maximum lysis (addition of Triton-X) and spontaneous lysis (without
effector cells). All measurements are done in quadruplicates.
Measurement of chromium activity in the supernatants is performed
with a Wizard 3'' gammacounter (Perkin Elmer Life Sciences GmbH,
Koln, Germany). Analysis of the experimental data is performed with
Prism 4 for Windows (version 4.02, GraphPad Software Inc., San
Diego, California, USA). Sigmoidal dose response curves typically
have R.sup.2 values >0.90 as determined by the software. EC50
values calculated by the analysis program are used for comparison
of bioactivity.
[0626] Only those constructs showing potent recruitment of
cytotoxic activity of effector T cells against target cells
positive for Endosialin are selected for further use.
8.15 Generation of CHO Cells Expressing Macaque Endosialin
[0627] The cDNA sequence of macaque Endosialin is obtained by a set
of 2 PCRs on cDNA from macaque monkey colon prepared according to
standard protocols. The following reaction conditions: 1 cycle at
95.degree. C. for 5 minutes followed by 40 cycles with 95.degree.
C. for 45 seconds, 50.degree. C. for 45 seconds and 72.degree. C.
for 2 minutes followed by a terminal cycle of 72.degree. C. for 5
minutes and the following primers are used for the first PCR:
TABLE-US-00011 forward primer: SEQ ID NO: 418
5'-atatgaattcgccaccatgctgctgcgcctgttgctggcc-3' reverse primer: SEQ
ID NO: 419 5'-gtcttcatcttcctcatcctcccc-3'
[0628] The following reaction conditions: 1 cycle at 95.degree. C.
for 5 minutes followed by 40 cycles with 95.degree. C. for 45
seconds, 58.degree. C. for 45 seconds and 72.degree. C. for 2
minutes followed by a terminal cycle of 72.degree. C. for 5 minutes
and the following primers are used for the second PCR:
TABLE-US-00012 forward primer: SEQ ID NO: 420
5'-gtcaactacgttggtggcttcgagtg-3' reverse primer: SEQ ID NO: 421
5'-ggtctagatcacttatcgtcatcatctttgtagtccacgctggttc
tgcaggtctgc-3'
[0629] The PCR reactions are performed under addition of PCR grade
betain to a final concentration of 1 M. Those PCRs generate two
overlapping fragments, which are isolated and sequenced according
to standard protocols using the PCR primers, and thereby provided a
portion of the cDNA sequence coding macaque Endosialin from codon 9
of the leader peptide to codon 733 of the mature protein. To
generate a construct for expression of macaque Endosialin a cDNA
fragment is obtained by gene synthesis according to standard
protocols (the cDNA and amino acid sequence of the construct is
listed under SEQ ID Nos 422 and 423). In this construct the coding
sequence of macaque Endosialin from amino acid 9 of the leader
peptide to amino acid 733 of the mature protein, followed in frame
by the coding sequence of amino acid 734 to the last amino acid of
the mature human Endosialin protein, followed in frame by the
coding sequence of a FLAG tag and a stop codon is fused in frame to
the coding sequence of the amino acids 1 to 8 of the leader peptide
of the human Endosialin protein. The gene synthesis fragment is
also designed as to contain a Kozak site for eukaryotic expression
of the construct and restriction sites at the beginning and the end
of the fragment containing the cDNA. The introduced restriction
sites, EcoRI at the 5' end and XbaI at the 3' end, are utilised in
the following cloning procedures. The gene synthesis fragment is
cloned via EcoRI and XbaI into a plasmid designated pEF-DHFR
(pEF-DHFR is described in Raum et al. Cancer Immunol Immunother 50
(2001) 141-150) following standard protocols. The aforementioned
procedures are carried out according to standard protocols
(Sambrook, Molecular Cloning; A Laboratory Manual, 3rd edition,
Cold Spring Harbour Laboratory Press, Cold Spring Harbour, New York
(2001)). A clone with sequence-verified nucleotide sequence is
transfected into DHFR deficient CHO cells for eukaryotic expression
of the construct. Eukaryotic protein expression in DHFR deficient
CHO cells is performed as described by Kaufmann R. J. (1990)
Methods Enzymol. 185, 537-566. Gene amplification of the construct
is induced by increasing concentrations of methotrexate (MTX) to a
final concentration of up to 20 nM MTX.
8.16 Flow Cytometric Analysis of Cross-Species Specificity of
Bispecific Antibodies Directed at Membrane-Proximal Target Epitopes
of Human Endosialin
[0630] In order to test the cross-species specificity of bispecific
antibodies directed at membrane-proximal target epitopes of human
Endosialin the capability of the constructs to bind to macaque
Endosialin and macaque CD3, respectively, is investigated by FACS
analysis. For this purpose the macaque Endosialin transfected CHO
cells as described in example 8.15 and the macaque T cell line
4119LnPx (kindly provided by Prof Fickenscher, Hygiene Institute,
Virology, Erlangen-Nuernberg; published in Knappe A, et al., and
Fickenscher H., Blood 2000, 95, 3256-61) are used. 200.000 cells of
the respective cell lines are incubated for 30 min on ice with with
50 .mu.l of cell culture supernatant of transfected cells
expressing the cross-species specific bispecific antibody
constructs. The cells are washed twice in PBS with 2% FCS and
binding of the construct is detected with a murine Penta His
antibody (Qiagen; diluted 1:20 in 50 .mu.l PBS with 2% FCS). After
washing, bound anti His antibodies are detected with an Fc
gamma-specific antibody (Dianova) conjugated to phycoerythrin,
diluted 1:100 in PBS with 2% FCS. Supernatant of untransfected
cells is used as a negative control.
[0631] Flow cytometry is performed on a FACS-Calibur apparatus, the
CellQuest software is used to acquire and analyze the data (Becton
Dickinson biosciences, Heidelberg). FACS staining and measuring of
the fluorescence intensity are performed as described in Current
Protocols in Immunology (Coligan, Kruisbeek, Margulies, Shevach and
Strober, Wiley-Interscience, 2002).
9. Generation of Bispecific Single Chain Antibodies Directed at
Membrane-Proximal Target Epitopes of Human IGF-1R
9.1 Generation of CHO Cells Expressing Human IGF-1R
[0632] The coding sequence of human IGF-1R as published in GenBank
(Accession number NM_000875) is obtained by gene synthesis
according to standard protocols. The gene synthesis fragment is
designed as to contain first a Kozak site for eukaryotic expression
of the construct followed by the coding sequence of the human
IGF-1R protein and a stop codon (the cDNA and amino acid sequence
of the construct is listed under SEQ ID Nos 424 and 425). The gene
synthesis fragment is also designed as to introduce restriction
sites at the beginning and at the end of the fragment. The
introduced restriction sites, EcoRI at the 5' end and SalI at the
3' end, are utilized in the following cloning procedures. An
internal restriction site is removed by silent mutation of the
coding sequence in the gene synthesis fragment (BspEl: nucleotide
18 from A to C). The gene synthesis fragment is cloned via EcoRI
and SalI into a plasmid designated pEF-DHFR (pEF-DHFR is described
in Raum et al. Cancer Immunol Immunother 50 (2001) 141-150)
following standard protocols. The aforementioned procedures are
carried out according to standard protocols (Sambrook, Molecular
Cloning; A Laboratory Manual, 3rd edition, Cold Spring Harbour
Laboratory Press, Cold Spring Harbour, New York (2001)). A clone
with sequence-verified nucleotide sequence is transfected into DHFR
deficient CHO cells for eukaryotic expression of the construct.
Eukaryotic protein expression in DHFR deficient CHO cells is
performed as described by Kaufmann R. J. (1990) Methods Enzymol.
185, 537-566. Gene amplification of the construct is induced by
increasing concentrations of methotrexate (MTX) to a final
concentration of up to 20 nM MTX.
9.2 Generation of a Soluble Human IGF-1R Fusion Protein
[0633] The modified coding sequence of human IGF-1R as described in
Example 9.1 is used for the construction of an artificial cDNA
sequence encoding a soluble fusion protein of human IGF-1R and
murine IgG1 Fc. To generate a construct for expression of the
soluble human IGF-1R fusion protein .alpha. cDNA fragment is
obtained by gene synthesis according to standard protocols (the
cDNA and amino acid sequence of the construct is listed under SEQ
ID Nos 426 and 427). The gene synthesis fragment is designed as to
contain first a Kozak site for eukaryotic expression of the
construct followed by the coding sequence of the human IGF-1R
protein from amino acid 1 to 935 corresponding to the signal
peptide and extracellular domains of human IGF-1R, followed in
frame by the coding sequence of an artificial
Ser.sub.1-Gly.sub.4-Ser.sub.1-linker, followed in frame by the
coding sequence of the hinge region and Fc gamma portion of murine
IgG1, followed in frame by the coding sequence of a 6 histidine tag
and a stop codon. The gene synthesis fragment is also designed as
to introduce restriction sites at the beginning and at the end of
the fragment. The introduced restriction sites, EcoRI at the 5' end
and SalI at the 3' end, are utilized in the following cloning
procedures. The gene synthesis fragment is cloned via EcoRI and
SalI into a plasmid designated pEF-DHFR (pEF-DHFR is described in
Raum et al. Cancer Immunol Immunother 50 (2001) 141-150) following
standard protocols. The aforementioned procedures are all carried
out according to standard protocols (Sambrook, Molecular Cloning; A
Laboratory Manual, 3rd edition, Cold Spring Harbour Laboratory
Press, Cold Spring Harbour, New York (2001)). A clone with
sequence-verified nucleotide sequence is transfected into DHFR
deficient CHO cells for eukaryotic expression of the construct.
Eukaryotic protein expression in DHFR deficient CHO cells is
performed as described by Kaufmann R. J. (1990) Methods Enzymol.
185, 537-566. Gene amplification of the construct is induced by
increasing concentrations of methotrexate (MTX) to a final
concentration of up to 20 nM MTX. After two passages of stationary
culture the cells are grown in roller bottles with nucleoside-free
HyQ PF CHO liquid soy medium (with 4.0 mM L-Glutamine with 0.1%
Pluronic F--68; HyClone) for 7 days before harvest. The cells are
removed by centrifugation and the supernatant containing the
expressed protein is stored at -20.degree. C. Alternatively a clone
of the expression plasmid with sequence-verified nucleotide
sequence is used for transfection and protein expression in the
FreeStyle 293 Expression System (Invitrogen GmbH, Karlsruhe,
Germany) according to the manufacturer's protocol. Supernatant
containing the expressed protein is obtained, cells are removed by
centrifugation and the supernatant is stored at -20.degree. C. For
purification of the soluble human IGF-1R fusion protein .alpha.
goat anti-mouse Fc affinity column is prepared according to
standard protocols using a commercially available affinity purified
goat anti-mouse IgG Fc fragment specific antibody with minimal
cross-reaction to human, bovine and horse serum proteins (Jackson
ImmunoResearch Europe Ltd.). Using this affinity column the fusion
protein is isolated out of cell culture supernatant on an Akta
Explorer System (GE Amersham) and eluted by citric acid. The eluate
is neutralized and concentrated.
9.3 Generation of CHO Cells Expressing Murine IGF-1R
[0634] The sequence of murine IGF-1R (NM_010513 Mus musculus
insulin-like growth factor I receptor (Igf1r), mRNA, National
Center for Biotechnology Information,
http://www.ncbi.nlm.nih.gov/entrez) is used to obtain a synthetic
cDNA molecule by gene synthesis according to standard protocols.
The gene synthesis fragment is designed as to contain the coding
sequence of an immunoglobulin heavy chain leader comprising a start
codon embedded within a Kozak consensus sequence, followed in frame
by the coding sequence of a FLAG tag, followed in frame by the
complete coding sequence of mature murine IGF-1R (the cDNA and
amino acid sequence of the construct is listed under SEQ ID Nos 428
and 429). The gene synthesis fragment is also designed as to
introduce restriction sites at the 5' end (EcoRI) and at the 3' end
(Sal I) of the cDNA fragment for cloning into the mammalian cell
expression vector pEF-DHFR (pEF-DHFR is described in Raum et al.
Cancer Immunol Immunother 50 (2001) 141-150). The aforementioned
procedures are carried out according to standard protocols
(Sambrook, Molecular Cloning; A Laboratory Manual, 3rd edition,
Cold Spring Harbour Laboratory Press, Cold Spring Harbour, New York
(2001)). A clone with sequence-verified nucleotide sequence is
transfected into DHFR deficient CHO cells for eukaryotic expression
of the construct. Eukaryotic protein expression in DHFR deficient
CHO cells is performed as described by Kaufmann R. J. (1990)
Methods Enzymol. 185, 537-566. Gene amplification for increased
antigen expression is induced by increasing concentrations of
methotrexate (MTX) to a final concentration of up to 20 nM MTX.
9.4 Generation of CHO Cells Expressing a Mutated Human IGF-1R
Antigen with Murine Membrane-Distal Epitopes
[0635] The coding sequence of a mutated human IGF-1R antigen with
murine membrane-distal epitopes is obtained by gene synthesis
according to standard protocols. The gene synthesis fragment is
designed as to contain the coding sequence of an immunoglobulin
heavy chain leader comprising a start codon embedded within a Kozak
consensus sequence, followed in frame by the coding sequence of a
FLAG tag, followed in frame by the coding sequence of the L1 domain
and the cysteine-rich domain of mature murine IGF-1R followed in
frame by human IGF-1R from the L2 domain to the stop codon (the
cDNA and amino acid sequence of the construct is listed under SEQ
ID Nos 430 and 431). The gene synthesis fragment is also designed
as to introduce restriction sites at the 5' end (EcoRI) and at the
3' end (Sal I) of the cDNA fragment for cloning into the mammalian
cell expression vector pEF-DHFR (pEF-DHFR is described in Raum et
al. Cancer Immunol Immunother 50 (2001) 141-150). The
aforementioned procedures are carried out according to standard
protocols (Sambrook, Molecular Cloning; A Laboratory Manual, 3rd
edition, Cold Spring Harbour Laboratory Press, Cold Spring Harbour,
New York (2001)). A clone with sequence-verified nucleotide
sequence is transfected into DHFR deficient CHO cells for
eukaryotic expression of the construct. Eukaryotic protein
expression in DHFR deficient CHO cells is performed as described by
Kaufmann R. J. (1990) Methods Enzymol. 185, 537-566. Gene
amplification for increased antigen expression is induced by
increasing concentrations of methotrexate (MTX) to a final
concentration of up to 20 nM MTX.
9.5 Generation of CHO Cells Expressing a Mutated Murine IGF-1R
Antigen with Human Membrane-Distal Epitopes
[0636] The coding sequence of a mutated murine IGF-1R antigen with
human membrane-distal epitopes is obtained by gene synthesis
according to standard protocols. The gene synthesis fragment is
designed as to contain the coding sequence of an immunoglobulin
heavy chain leader comprising a start codon embedded within a Kozak
consensus sequence, followed in frame by the coding sequence of a
FLAG tag, followed in frame by the L1 domain and the cysteine-rich
domain of mature human IGF-1R followed in frame by murine IGF-1R
from the L2 domain to the stop codon (the cDNA and amino acid
sequence of the construct is listed under SEQ ID Nos 432 and 433).
The gene synthesis fragment is also designed as to introduce
restriction sites at the 5' end (EcoRI) and at the 3' end (Sal I)
of the cDNA fragment for cloning into the mammalian cell expression
vector pEF-DHFR (pEF-DHFR is described in Raum et al. Cancer
Immunol Immunother 50 (2001) 141-150). The aforementioned
procedures are carried out according to standard protocols
(Sambrook, Molecular Cloning; A Laboratory Manual, 3rd edition,
Cold Spring Harbour Laboratory Press, Cold Spring Harbour, New York
(2001)). A clone with sequence-verified nucleotide sequence is
transfected into DHFR deficient CHO cells for eukaryotic expression
of the construct. Eukaryotic protein expression in DHFR deficient
CHO cells is performed as described by Kaufmann R. J. (1990)
Methods Enzymol. 185, 537-566. Gene amplification for increased
antigen expression is induced by increasing concentrations of
methotrexate (MTX) to a final concentration of up to 20 nM MTX.
9.6 Immunization of Mice Using a Soluble Human IGF-1R Fusion
Protein
[0637] Twelve weeks old F1 mice from BALB/c.times.C57BL/6 crossings
are immunized with the soluble human IGF-1R fusion protein as
described in Example 9.2. To this end for each animal 40 .mu.g of
the soluble human IGF-1R fusion protein are mixed with 10 nmol of a
thioate-modified CpG-Oligonucleotide (5'-tccatgacgttcctgatgct-3')
in 300 .mu.l PBS and are injected intraperitoneally. Mice receive
booster immunizations after 21, 42 and optionally 63 days in the
same way. Ten days after the first booster immunization, blood
samples are taken and antibody serum titers against human IGF-1R
are tested by flow cytometry according to standard protocols. To
this end 200.000 cells of the human IGF-1R transfected CHO cells as
described in Example 9.1 are incubated for 30 min on ice with 50
.mu.l of serum of the immunized animals diluted 1:1000 in PBS with
2% FCS. The cells are washed twice in PBS with 2% FCS and binding
of serum antibodies is detected with an mouse Fc gamma-specific
antibody (Dianova) conjugated to phycoerythrin, diluted 1:100 in
PBS with 2% FCS. Serum of the animals obtained prior to
immunization is used as a negative control. Flow cytometry is
performed on a FACS-Calibur apparatus, the CellQuest software is
used to acquire and analyze the data (Becton Dickinson biosciences,
Heidelberg). FACS staining and measuring of the fluorescence
intensity are performed as described in Current Protocols in
Immunology (Coligan, Kruisbeek, Margulies, Shevach and Strober,
Wiley-Interscience, 2002).
[0638] Animals demonstrating significant serum reactivity against
human IGF-1R as determined by the FACS analysis are used in the
subsequent experiment.
9.7 Generation of an Immune Murine Antibody scFv Library:
Construction of a Combinatorial Antibody Library and Phage
Display
[0639] Three days after the last booster immunization spleen cells
of reactive animals are harvested for the preparation of total RNA
according to standard protocols.
[0640] A library of murine immunoglobulin (Ig) light chain (kappa)
variable region (VK) and Ig heavy chain variable region (VH)
DNA-fragments is constructed by RT-PCR on murine spleen RNA using
VK- and VH specific primers. cDNA is synthesized according to
standard protocols, see example 2.7.
[0641] 450 ng of the kappa light chain fragments (SacI-SpeI
digested) are ligated with 1400 ng of the phagemid pComb3H5Bhis
(SacI-SpeI digested; large fragment). The resulting combinatorial
antibody library is then transformed into 300 .mu.l of
electrocompetent Escherichia coli XL1 Blue cells by electroporation
(2.5 kV, 0.2 cm gap cuvette, 25 .mu.FD, 200 Ohm, Biorad
gene-pulser) resulting in a library size of more than 10.sup.7
independent clones. After one hour of phenotype expression,
positive transformants are selected for carbenicillin resistance
encoded by the pComb3H5BHis vector in 100 ml of liquid super broth
(SB)-culture over night. Cells are then harvested by centrifugation
and plasmid preparation is carried out using a commercially
available plasmid preparation kit (Qiagen).
[0642] 2800 ng of this plasmid-DNA containing the VK-library
(XhoI-BstElI digested; large fragment) are ligated with 900 ng of
the heavy chain V-fragments (XhoI-BstElI digested) and again
transformed into two 300 .mu.l aliquots of electrocompetent E. coli
XL1 Blue cells by electroporation (2.5 kV, 0.2 cm gap cuvette, 25
.mu.FD, 200 Ohm) resulting in a total VH-VK scFv (single chain
variable fragment) library size of more than 10.sup.7 independent
clones.
[0643] After phenotype expression and slow adaptation to
carbenicillin, the E. coli cells containing the antibody library
are transferred into SB-Carbenicillin (SB with 50 .mu.g/mL
carbenicillin) selection medium. The E. coli cells containing the
antibody library are then infected with an infectious dose of
10.sup.12 particles of helper phage VCSM13 resulting in the
production and secretion of filamentous M13 phage, wherein each
phage particle contains single stranded pComb3H5BHis-DNA encoding a
murine scFv-fragment and displays the corresponding scFv-protein as
a translational fusion to phage coat protein III. This pool of
phages displaying the antibody library is later used for the
selection of antigen binding entities.
9.8 Phage Display Based Selection of Membrane-Proximal Target
Binders on CHO Cells Expressing the Mutated Human IGF-1R Antigen
with Murine Membrane-Distal Epitopes
[0644] The phage library carrying the cloned scFv-repertoire is
harvested from the respective culture supernatant by PEG8000/NaCl
precipitation and centrifugation. Approximately 10.sup.11 to
10.sup.12 scFv phage particles are resuspended in 0.4 ml of
PBS/0.1% BSA and incubated with 10.sup.5 to 10.sup.7 CHO cells
expressing the mutated human IGF-1R antigen with murine
membrane-distal epitopes as described in example 9.4 for 1 hour on
ice under slow agitation. These CHO cells are grown beforehand,
harvested by centrifugation, washed in PBS and resuspended in
PBS/1% FCS (containing Na Azide). scFv phage which do not
specifically bind to the CHO cells are eliminated by up to five
washing steps with PBS/1% FCS (containing Na Azide). After washing,
binding entities are eluted from the cells by resuspending the
cells in HCl-glycine pH 2.2 (10 min incubation with subsequent
vortexing) and after neutralization with 2 M Tris pH 12, the eluate
is used for infection of a fresh uninfected E. coli XL1 Blue
culture (OD600>0.5). The E. coli culture containing E. coli
cells successfully transduced with a phagemid copy, encoding a
murine scFv-fragment, are again selected for carbenicillin
resistance and subsequently infected with VCMS 13 helper phage to
start the second round of antibody display and in vitro selection.
Typically a total of 4 to 5 rounds of selections are carried
out.
9.9 Screening for Membrane-Proximal Target Binders on CHO Cells
Expressing the Human IGF-1R Antigen, the Murine IGF-1R Antigen and
the Mutated Murine IGF-1R Antigen with Human Membrane-Distal
Epitopes
[0645] Plasmid DNA corresponding to 4 and 5 rounds of panning is
isolated from E. coli cultures after selection. For the production
of soluble scFv-protein, VH-VL-DNA fragments are excised from the
plasmids (XhoI-SpeI). These fragments are cloned via the same
restriction sites in the plasmid pComb3H5BFlag/His differing from
the original pComb3H5BHis in that the expression construct (e.g.
scFv) includes a Flag-tag (TGDYKDDDDK) between the scFv and the
His6-tag and the additional phage proteins are deleted. After
ligation, each pool (different rounds of panning) of plasmid DNA is
transformed into 100 .mu.l heat shock competent E. coli TG1 or XLI
blue and plated onto carbenicillin LB-agar. Single colonies are
picked into 100 .mu.l of LB carb (LB with 50 .mu.g/ml
carbenicillin).
[0646] After induction with 1 mM IPTG E. coli transformed with
pComb3H5BFlag/His containing a VL- and VH-segment produce soluble
scFv in sufficient amounts. Due to a suitable signal sequence, the
scFv is exported into the periplasma where it folds into a
functional conformation.
[0647] Single E. coli bacterial colonies from the transformation
plates are picked for periplasmic small scale preparations and
grown in SB-medium (e.g. 10 ml) supplemented with 20 mM MgCl.sub.2
and carbenicillin 50 .mu.g/ml (and re-dissolved in PBS (e.g. 1 ml)
after harvesting. A temperature shock is applied by four rounds of
freezing at -70.degree. C. and thawing at 37.degree. C. whereby the
outer membrane of the bacteria is destroyed and the soluble
periplasmic proteins including the scFvs are released into the
supernatant. After elimination of intact cells and cell-debris by
centrifugation, the supernatant containing the murine anti-human
IGF-1R-scFvs is collected and used for further examination.
[0648] Screening of the isolated scFvs for membrane-proximal target
binders is performed by flow cytometry on CHO cells expressing the
human IGF-1R antigen as described in Example 9.1, the murine IGF-1R
antigen as described in Example 9.3 and the mutated murine IGF-1R
antigen with human membrane-distal epitopes as described in Example
9.5.
[0649] For flow cytometry 2.5.times.10.sup.5 cells of the
respective cell lines are incubated with 50 .mu.l supernatant. The
binding of the constructs is detected with an anti-His antibody
(Penta-His Antibody, BSA free, Qiagen GmbH, Hilden, FRG) at 2
.mu.g/ml in 50 .mu.l PBS with 2% FCS. As a second step reagent a
R-Phycoerythrin-conjugated affinity purified F(ab')2 fragment, goat
anti-mouse IgG (Fc-gamma fragment specific), diluted 1:100 in 50
.mu.l PBS with 2% FCS (Dianova, Hamburg, FRG) is used. The samples
are measured on a FACSscan (BD biosciences, Heidelberg, FRG).
[0650] Only constructs which show binding to CHO cells expressing
the human IGF-1R antigen and do not show binding to CHO cells
expressing the murine IGF-1R antigen and also do not show binding
to CHO cells expressing the mutated murine IGF-1R antigen with
human membrane-distal epitopes are selected for further use.
9.10 Generation of Human/Humanized Equivalents of Non-Human scFvs
to Membrane-Proximal Target Epitopes of Human IGF-1R
[0651] The VH region of a murine anti-IGF-1R scFv to a
membrane-proximal target epitope of human IGF-1R is aligned against
human antibody germline amino acid sequences. The human antibody
germline VH sequence is chosen which has the closest homology to
the non-human VH and a direct alignment of the two amino acid
sequences is performed. There are a number of framework residues of
the non-human VH that differ from the human VH framework regions
("different framework positions"). Some of these residues may
contribute to the binding and activity of the antibody to its
target.
[0652] To construct a library that contains the murine CDRs and at
every framework position that differs from the chosen human VH
sequence both possible residues (the human and the maternal murine
amino acid residue), degenerated oligonucleotides are synthesized.
These oligonucleotides incorporate at the differing positions the
human residue with a probability of 75% and the murine residue with
a probability of 25%. For one human VH e.g. six of these
oligonucleotides have to be synthesized that overlap in a terminal
stretch of approximately 20 nucleotides. To this end every second
primer is an antisense primer. Restriction sites within the
oligonucleotides needed for later cloning are deleted.
[0653] These primers may have a length of 60 to 90 nucleotides,
depending on the number of primers that are needed to span over the
whole V sequence.
[0654] These e.g. six primers are mixed in equal amounts (e.g. 1
.mu.l of each primer (primer stocks 20 to 100 .mu.M) to a 20 .mu.l
PCR reaction) and added to a PCR mix consisting of PCR buffer,
nucleotides and Taq polymerase. This mix is incubated at 94.degree.
C. for 3 minutes, 65.degree. C. for 1 minute, 62.degree. C. for 1
minute, 59.degree. C. for 1 minute, 56.degree. C. for 1 minute,
52.degree. C. for 1 minute, 50.degree. C. for 1 minute and at
72.degree. C. for 10 minutes in a PCR cycler. Subsequently the
product is run in an agarose gel electrophoresis and the product of
a size from 200 to 400 base pairs isolated from the gel according
to standard methods.
[0655] This PCR product is then used as a template for a standard
PCR reaction using primers that incorporate suitable N-terminal and
C-terminal cloning restriction sites. The DNA fragment of the
correct size (for a VH approximately 350 nucleotides) is isolated
by agarose gel electrophoresis according to standard methods. In
this way sufficient VH DNA fragment is amplified. This VH fragment
is now a pool of VH fragments that have each one a different amount
of human and murine residues at the respective differing framework
positions (pool of humanized VH). The same procedure is performed
for the VL region of the murine anti-IGF-1R scFv to a
membrane-proximal target epitope of human IGF-1R (pool of humanized
VL).
[0656] The pool of humanized VH is then combined with the pool of
humanized VL in the phage display vector pComb3H5Bhis to form a
library of functional scFvs from which after display on filamentous
phage--anti-IGF-1R binders to membrane-proximal target epitopes of
human IGF-1R are selected, screened, identified and confirmed as
described above for the parental non-human (murine) anti-IGF-1R
scFv. Single clones are then analyzed for favorable properties and
amino acid sequence. Those scFvs, which are closest in amino acid
sequence homology to human germline V-segments, are preferred.
[0657] Human/humanized anti-IGF-1R scFvs to membrane-proximal
target epitopes of human IGF-1R are converted into recombinant
bispecific single chain antibodies and further characterized as
follows.
9.11 Generation of I2C-Based Bispecific Single Chain Antibodies
Directed at Membrane-Proximal Target Epitopes of Human IGF-1R
[0658] Anti-IGF-1R scFvs to membrane-proximal target epitopes of
human IGF-1R with favorable properties and amino acid sequence are
converted into recombinant bispecific single chain antibodies by
joining them via a Gly.sub.4Ser.sub.1-linker with the CD3 specific
scFv I2C (SEQ ID) to result in constructs with the domain
arrangement
VH.sub.IGF-1R-(Gly.sub.4Ser.sub.1).sub.3-VL.sub.IGF-1R-Ser.sub.1Gly.sub.4-
Ser.sub.1-VH.sub.CD3-(Gly.sub.4Ser.sub.1).sub.3-VL.sub.CD3.
[0659] I2C-based bispecific single chain antibodies directed at
membrane-proximal target epitopes of human IGF-1R were designed as
set out in the following Table 8:
TABLE-US-00013 TABLE 8 Formats of I2C-based bispecific single chain
antibodies directed at membrane-proximal target epitopes of human
IGF-1R SEQ ID Formats of protein constructs (nucl/prot) (N .fwdarw.
C) 848/847 IGF1R12HL .times. I2CHL 862/861 IGF1R24HL .times.
I2CHL
[0660] Alternatively further constructs with different domain
arrangements can be generated according to standard protocolls. For
expression in CHO cells the coding sequences of (i) an N-terminal
immunoglobulin heavy chain leader comprising a start codon embedded
within a Kozak consensus sequence and (ii) a C-terminal His6-tag
followed by a stop codon are both attached in frame to the
nucleotide sequence encoding the bispecific single chain antibodies
prior to insertion of the resulting DNA-fragment as obtained by
gene synthesis into the multiple cloning site of the expression
vector pEF-DHFR (Raum et al. Cancer Immunol Immunother 50 (2001)
141-150). A clone with sequence-verified nucleotide sequence is
transfected into DHFR deficient CHO cells for eukaryotic expression
of the construct. Eukaryotic protein expression in DHFR deficient
CHO cells is performed as described by Kaufmann R. J. (1990)
Methods Enzymol. 185, 537-566. Gene amplification of the construct
is induced by increasing concentrations of methotrexate (MTX) to a
final concentration of up to 20 nM MTX.
9.12 Expression and Purification of Bispecific Single Chain
Antibody Molecules Directed at Membrane-Proximal Target Epitopes of
Human IGF-1R
[0661] Bispecific single chain antibody molecules are expressed in
Chinese hamster ovary cells (CHO). Eukaryotic protein expression in
DHFR deficient CHO cells is performed as described by Kaufmann R.
J. (1990) Methods Enzymol. 185, 537-566. Gene amplification of the
constructs is induced by addition of increasing concentrations of
MTX up to final concentrations of 20 nM MTX. After two passages of
stationary culture cell culture supernatant is collected and used
in the subsequent experiments. To generate supernatant for
purification after two passages of stationary culture the cells are
grown in roller bottles with nucleoside-free HyQ PF CHO liquid soy
medium (with 4.0 mM L-Glutamine with 0.1% Pluronic F-68; HyClone)
for 7 days before harvest. The cells are removed by centrifugation
and the supernatant containing the expressed protein is stored at
-20.degree. C. Alternatively, constructs are transiently expressed
in HEK 293 cells. Transfection is performed with 293fectin reagent
(Invitrogen, #12347-019) according to the manufacturer's protocol.
Furthermore the constructs are alternatively expressed in
transiently transfected DHFR deficient CHO cells using for example
FuGENE.RTM. HD Transfection Reagent (Roche Diagnostics GmbH, Cat.
No. 04709691001) according to the manufacturer's protocol.
Akta.RTM. Explorer System (GE Health Systems) and Unicorn.RTM.
Software are used for chromatography. Immobilized metal affinity
chromatography ("IMAC") is performed using a Fractogel EMD
Chelate.RTM. (Merck) which is loaded with ZnCl.sub.2 according to
the protocol provided by the manufacturer. The column is
equilibrated with buffer A (20 mM sodium phosphate buffer pH 7.2,
0.1 M NaCl) and the cell culture supernatant (500 ml) is applied to
the column (10 ml) at a flow rate of 3 ml/min. The column is washed
with buffer A to remove unbound sample. Bound protein is eluted
using a two step gradient of buffer B (20 mM sodium phosphate
buffer pH 7.2, 0.1 M NaCl, 0.5 M Imidazole) according to the
following procedure:
Step 1: 20% buffer B in 6 column volumes Step 2: 100% buffer B in 6
column volumes
[0662] Eluted protein fractions from step 2 are pooled for further
purification. All chemicals are of research grade and purchased
from Sigma (Deisenhofen) or Merck (Darmstadt).
[0663] Gel filtration chromatography is performed on a HiLoad 16/60
Superdex 200 prep grade column (GE/Amersham) equilibrated with
Equi-buffer (25 mM Citrate, 200 mM Lysine, 5% Glycerol, pH 7.2).
Eluted protein samples (flow rate 1 ml/min) are subjected to
standard SDS-PAGE and Western Blot for detection. Prior to
purification, the column is calibrated for molecular weight
determination (molecular weight marker kit, Sigma MW GF-200).
Protein concentrations are determined using OD280 nm.
[0664] Purified bispecific single chain antibody protein is
analyzed in SDS PAGE under reducing conditions performed with
pre-cast 4-12% Bis Tris gels (Invitrogen). Sample preparation and
application are performed according to the protocol provided by the
manufacturer. The molecular weight is determined with MultiMark
protein standard (Invitrogen). The gel is stained with colloidal
Coomassie (Invitrogen protocol). The purity of the isolated protein
is typically >95% as determined by SDS-PAGE.
[0665] The bispecific single chain antibody has a molecular weight
of about 52 kDa under native conditions as determined by gel
filtration in PBS.
[0666] Western Blot is performed using an Optitran.RTM. BA-S83
membrane and the Invitrogen Blot Module according to the protocol
provided by the manufacturer. The antibody used is directed against
the His Tag (Penta His, Qiagen) and a Goat-anti-mouse Ig labeled
with alkaline phosphatase (AP) (Sigma) is used as second step
reagent, and BCIP/NBT (Sigma) as substrate. A band detected at 52
kD corresponds to purified bispecific single chain antibodies.
[0667] 9.13 Flow Cytometric Binding Analysis of Bispecific
Antibodies Directed at Membrane-Proximal Target Epitopes of Human
IGF-1R
[0668] In order to test the functionality of bispecific antibody
constructs regarding the capability to bind to CD3 and to
membrane-proximal target epitopes of human IGF-1R, respectively, a
FACS analysis is performed. For this purpose CHO cells transfected
with human IGF-1R as described in Example 9.1 and the human CD3
positive T cell leukemia cell line HPB-ALL (DSMZ, Braunschweig,
ACC483) are used. For confirmation of binding to membrane-proximal
target epitopes of human IGF-1R--in addition--CHO cells expressing
the murine IGF-1R antigen as described in Example 9.3, CHO cells
expressing the mutated human IGF-1R antigen with murine
membrane-distal epitopes as described in Example 9.4 and CHO cells
expressing the mutated murine IGF-1R antigen with human
membrane-distal epitopes as described in Example 9.5 are used.
200.000 cells of the respective cell lines are incubated for 30 min
on ice with 50 .mu.l of cell culture supernatant of transfected
cells expressing the bispecific antibody constructs. The cells are
washed twice in PBS with 2% FCS and binding of the construct is
detected with a murine Penta His antibody (Qiagen; diluted 1:20 in
50 .mu.l PBS with 2% FCS). After washing, bound anti His antibodies
are detected with an Fc gamma-specific antibody (Dianova)
conjugated to phycoerythrin, diluted 1:100 in PBS with 2% FCS.
Supernatant of untransfected cells is used as a negative
control.
[0669] Flow cytometry is performed on a FACS-Calibur apparatus, the
CellQuest software is used to acquire and analyze the data (Becton
Dickinson biosciences, Heidelberg). FACS staining and measuring of
the fluorescence intensity are performed as described in Current
Protocols in Immunology (Coligan, Kruisbeek, Margulies, Shevach and
Strober, Wiley-Interscience, 2002).
[0670] Only those constructs that show bispecific binding to human
CD3 as well as to human IGF-1R and neither bind to the murine
IGF-1R antigen nor to the mutated murine IGF-1R antigen with human
membrane-distal epitopes are selected for further use.
[0671] The bispecific binding of the single chain molecules listed
above was clearly detectable as shown in FIG. 17. In the FACS
analysis all constructs showed binding to human CD3 and human
IGF-1R compared to the negative control. Membrane-proximal target
binding of the single chain molecules listed above was clearly
detectable as shown in FIG. 19. In the FACS analysis all constructs
showed binding to the mutated human IGF-1R antigen with murine
membrane-distal epitopes and did not show binding to the murine
IGF-1R antigen and did also not show binding to the mutated murine
IGF-1R antigen with human membrane-distal epitopes as compared to
the negative control.
[0672] 9.14 Bioactivity of bispecific antibodies directed at
membrane-proximal target epitopes of human IGF-1R
[0673] Bioactivity of generated bispecific single chain antibodies
is analyzed by chromium 51 (51Cr) release in vitro cytotoxicity
assays using the CHO cells transfected with human IGF-1R described
in Example 9.1. As effector cells stimulated human CD4/CD56
depleted PBMC are used.
[0674] Stimulated human PBMC are obtained as follows:
[0675] A Petri dish (145 mm diameter, Greiner bio-one GmbH,
Kremsmunster) is coated with a commercially available anti-CD3
specific antibody (e.g. OKT3, Orthoclone) in a final concentration
of 1 .mu.g/ml for 1 hour at 37.degree. C. Unbound protein is
removed by one washing step with PBS. The fresh PBMC are isolated
from peripheral blood (30-50 ml human blood) by Ficoll gradient
centrifugation according to standard protocols. 3-5.times.10.sup.7
PBMC are added to the precoated petri dish in 120 ml of RPMI 1640
with stabilized glutamine/10% FCS/IL-2 20 U/ml (Proleukin, Chiron)
and stimulated for 2 days. On the third day the cells are collected
and washed once with RPMI 1640. IL 2 is added to a final
concentration of 20 U/ml and the cells are cultivated again for one
day in the same cell culture medium as above.
[0676] By depletion of CD4+ T cells and CD56+NK cells according to
standard protocols CD8+ cytotoxic T lymphocytes (CTLs) are
enriched.
[0677] Target cells are washed twice with PBS and labeled with 11.1
MBq 51Cr in a final volume of 100 .mu.l RPMI with 50% FCS for 60
minutes at 37.degree. C. Subsequently the labeled target cells are
washed 3 times with 5 ml RPMI and then used in the cytotoxicity
assay. The assay is performed in a 96 well plate in a total volume
of 250 .mu.l supplemented RPMI (as above) with an E:T ratio of
10:1. Supernatant of cells expressing the bispecific single chain
antibody molecules in a final concentration of 50% and 20 twofold
dilutions thereof are applied. The assay time is 18 hours.
Cytotoxicity is measured as relative values of released chromium in
the supernatant related to the difference of maximum lysis
(addition of Triton-X) and spontaneous lysis (without effector
cells). All measurements are done in quadruplicates. Measurement of
chromium activity in the supernatants is performed with a Wizard
3'' gammacounter (Perkin Elmer Life Sciences GmbH, Koln, Germany).
Analysis of the experimental data is performed with Prism 4 for
Windows (version 4.02, GraphPad Software Inc., San Diego, Calif.,
USA). Sigmoidal dose response curves typically have R.sup.2 values
>0.90 as determined by the software.
[0678] Only those constructs showing potent recruitment of
cytotoxic activity of effector T cells against target cells
positive for IGF-1R are selected for further use.
9.15 Generation of CHO Cells Expressing Macaque IGF-1R
[0679] The coding sequence of macaque IGF-1R as published in
GenBank (Accession number XM_001100407) is obtained by gene
synthesis according to standard protocols. The gene synthesis
fragment is designed as to contain first a Kozak site for
eukaryotic expression of the construct followed by the coding
sequence of the macaque IGF-1R protein and a stop codon (the cDNA
and amino acid sequence of the construct is listed under SEQ ID Nos
434 and 435). The gene synthesis fragment is also designed as to
introduce restriction sites at the beginning and at the end of the
fragment. The introduced restriction sites, EcoRI at the 5' end and
SalI at the 3' end, are utilized in the following cloning
procedures. The gene synthesis fragment is cloned via EcoRI and
SalI into a plasmid designated pEF-DHFR (pEF-DHFR is described in
Raum et al. Cancer Immunol Immunother 50 (2001) 141-150) following
standard protocols. The aforementioned procedures are carried out
according to standard protocols (Sambrook, Molecular Cloning; A
Laboratory Manual, 3rd edition, Cold Spring Harbour Laboratory
Press, Cold Spring Harbour, New York (2001)). A clone with
sequence-verified nucleotide sequence is transfected into DHFR
deficient CHO cells for eukaryotic expression of the construct.
Eukaryotic protein expression in DHFR deficient CHO cells is
performed as described by Kaufmann R. J. (1990) Methods Enzymol.
185, 537-566. Gene amplification of the construct is induced by
increasing concentrations of methotrexate (MTX) to a final
concentration of up to 20 nM MTX.
9.16 Flow Cytometric Analysis of Cross-Species Specificity of
Bispecific Antibodies Directed at Membrane-Proximal Target Epitopes
of Human IGF-1R
[0680] In order to test the cross-species specificity of bispecific
antibodies directed at membrane-proximal target epitopes of human
IGF-1R the capability of the constructs to bind to macaque IGF-1R
and macaque CD3, respectively, is investigated by FACS analysis.
For this purpose the macaque IGF-1R transfected CHO cells as
described in example 9.15 and the macaque T cell line 4119LnPx
(kindly provided by Prof Fickenscher, Hygiene Institute, Virology,
Erlangen-Nuernberg; published in Knappe A, et al., and Fickenscher
H., Blood 2000, 95, 3256-61) are used. 200.000 cells of the
respective cell lines are incubated for 30 min on ice with with 50
.mu.l of cell culture supernatant of transfected cells expressing
the cross-species specific bispecific antibody constructs. The
cells are washed twice in PBS with 2% FCS and binding of the
construct is detected with a murine Penta His antibody (Qiagen;
diluted 1:20 in 50 .mu.l PBS with 2% FCS). After washing, bound
anti His antibodies are detected with an Fc gamma-specific antibody
(Dianova) conjugated to phycoerythrin, diluted 1:100 in PBS with 2%
FCS. Supernatant of untransfected cells is used as a negative
control.
[0681] Flow cytometry is performed on a FACS-Calibur apparatus, the
CellQuest software is used to acquire and analyze the data (Becton
Dickinson biosciences, Heidelberg). FACS staining and measuring of
the fluorescence intensity are performed as described in Current
Protocols in Immunology (Coligan, Kruisbeek, Margulies, Shevach and
Strober, Wiley-Interscience, 2002).
[0682] The cross-species specific binding of the single chain
molecules listed above was clearly detectable as shown in FIG. 17.
In the FACS analysis all constructs showed binding to macaque CD3
and macaque IGF-1R compared to the negative control.
Human/humanized equivalents of scFvs specific for IGF-1R contained
in the bispecific single chain molecules are generated as described
herein. Cloning of binding molecules based on these human/humanized
scFvs and expression and purification of these bispecific single
chain molecules is performed as described above. Flow cytometric
analysis of bispecific binding and analysis of bioactivity by
chromium 51 (51Cr) release in vitro cytotoxicity assays is
performed as described above. Based on demonstrated bispecific
binding and recruited cytotoxicity binding molecules are selected
for further use.
Example 10
10.1. Generation of PSMA- and CD3-Directed Bispecific Single Chain
Antibodies
[0683] Bispecific single chain antibodes comprising either scFv
binding domain P7 against a PSMA-epitope with <60 .ANG.
membrane-distance or scFv binding domain D4 against a PSMA-epitope
with .gtoreq.60 .ANG. membrane-distance and the scFv binding domain
I2C directed at CD3epsilon on human T cells were obtained by gene
synthesis. The gene synthesis fragments were designed as to contain
first a Kozak site for eukaryotic expression of the construct,
followed by a 19 amino acid immunoglobulin leader peptide, followed
in frame by the coding sequence of the bispecific single chain
antibody, followed in frame by the coding sequence of a 6 histidine
tag and a stop codon. The variable region arrangements as well as
the SEQ ID Nos of the cDNA- and amino acid sequences are listed in
the table 9 below.
TABLE-US-00014 SEQ ID Formats of protein constructs (nucl/prot) (N
.fwdarw. C) 488/487 PSMA-P7 HL .times. I2C HL 474/473 PSMA-D4 HL
.times. I2C HL
[0684] The gene synthesis fragments were also designed as to
introduce suitable restriction sites at the beginning (EcoRI) and
at the end of the fragment (Sal I) for cloning of the gene
synthesis fragment into the mammalian cell expression vector
pEF-DHFR (pEF-DHFR is described in Raum et al. Cancer Immunol
Immunother 50 (2001) 141-150). The aforementioned procedures were
carried out according to standard protocols (Sambrook, Molecular
Cloning; A Laboratory Manual, 3rd edition, Cold Spring Harbour
Laboratory Press, Cold Spring Harbour, New York (2001)). A clone
with sequence-verified nucleotide sequence was transfected into
DHFR deficient CHO cells for eukaryotic expression of the
construct. Eukaryotic protein expression in DHFR deficient CHO
cells was performed as described by Kaufmann R. J. (1990) Methods
Enzymol. 185, 537-566. Gene amplification of the construct was
induced by increasing concentrations of methotrexate (MTX) to a
final concentration of up to 20 nM MTX. After two passages of
stationary culture cell culture supernatant was collected and used
in the subsequent experiments.
10.2 Epitope Mapping of the PSMA- and CD3-Reactive Bispecific
Single Chain Antibody Molecule PSMA-P7 HL.times.I2C HL
[0685] A PSMA-epitope with <60 .ANG. membrane-distance of
bispecific single chain antibody PSMA-P7 HL.times.I2C HL was
confirmed by epitope mapping using chimeric PSMA constructs.
10.2.1 Generation of CHO Cells Expressing Human/Rat PSMA
Chimeras
[0686] PSMA of rattus norvegicus, which is not bound by PSMA
bispecific single chain antibody PSMA-P7 HL.times.I2C HL, was used
for making chimeras with human PSMA. Thus, creating a chimera in
the region containing the binding epitope of a PSMA bispecific
single chain antibody leads to loss of binding of said bispecific
single chain antibody to the respective PSMA construct.
[0687] The coding sequence of human PSMA as published in GenBank
(Accession number NM_004476) and the coding sequence of rat PSMA
(NM_057185, Rattus norvegicus folate hydrolase (Folh1), mRNA,
National Center for Biotechnology Information,
http://www.ncbi.nlm.nih.gov/entrez) were used for generation of the
chimeric constructs.
[0688] A set of 6 chimeric cDNA constructs was designed and
generated by gene synthesis according to standard protocols. In the
constructs segments of the coding sequences for the amino acids 140
to 169, 281 to 284, 300 to 344, 589 to 617, 683 to 690 and 716 to
750, respectively, were exchanged for the homologous sequences of
rat PSMA.
[0689] Chimeric PSMA constructs were generated as described above
and designated as set out in the following Table 10:
TABLE-US-00015 TABLE 10 Designation of chimeric PSMA constructs SEQ
ID (nucl/prot) Designation 461/462 huPSMArat140-169 463/464
huPSMArat281-284 465/466 huPSMArat300-344 467/468 huPSMArat598-617
469/470 huPSMArat683-690 471/472 huPSMArat716-750
[0690] The gene synthesis fragments were designed as to contain
first a Kozak site for eukaryotic expression of the construct
followed by the coding sequence of the chimeric PSMA proteins,
followed in frame by the coding sequence of a FLAG-tag and a stop
codon. The gene synthesis fragments were also designed as to
introduce restriction sites at the beginning and at the end of the
fragments. The introduced restriction sites, EcoRI at the 5' end
and SalI at the 3' end, were utilized in the following cloning
procedures. Undesirable internal restriction sites were removed by
silent mutation of the coding sequence in the gene synthesis
fragments. The gene synthesis fragments were cloned via EcoRI and
SalI into a plasmid designated pEF-DHFR (pEF-DHFR is described in
Raum et al. Cancer Immunol Immunother 50 (2001) 141-150) following
standard protocols. The aforementioned procedures were carried out
according to standard protocols (Sambrook, Molecular Cloning; A
Laboratory Manual, 3rd edition, Cold Spring Harbour Laboratory
Press, Cold Spring Harbour, New York (2001)). A clone with
sequence-verified nucleotide sequence was transfected into DHFR
deficient CHO cells for eukaryotic expression of the construct.
Eukaryotic protein expression in DHFR deficient CHO cells was
performed as described by Kaufmann R. J. (1990) Methods Enzymol.
185, 537-566. Gene amplification of the construct was induced by
increasing concentrations of methotrexate (MTX) to a final
concentration of up to 20 nM MTX.
10.2.2 Flow Cytometric Binding Analysis for Epitope Mapping of the
PSMA- and CD3-Reactive Bispecific Single Chain Antibody Molecule
PSMA-P7 HL.times.I2C HL Using Chimeric PSMA Proteins
[0691] In order to determine the binding epitope of the PSMA
bispecific single chain antibody PSMA-P7 HL.times.I2C HL a FACS
analysis was performed. For this purpose CHO cells transfected with
human/rat chimeric PSMA molecules as described in Example 10.2.1
above were used. FACS analysis with supernatant of CHO cells
expressing PSMA-P7 HL.times.I2C HL was performed as described
herein. Detection of binding of PSMA-P7 HL.times.I2C HL was
performed using a murine Penta His antibody and as second step
reagent an Fc gamma-specific antibody conjugated to phycoerythrin.
Supernatant of untransfected cells was used as a negative control.
Supernatant of CHO cells expressing the bispecific single chain
antibody construct PSMA-D4 HL.times.I2C HL cross-reactive with rat
PSMA was used as control for expression of the chimeric PSMA
constructs.
[0692] As shown in FIG. 20 both PSMA bispecific single chain
antibodies, PSMA-P7 HL.times.I2C HL and PSMA-D4 HL.times.I2C HL,
showed binding to the chimeric constructs hu PSMArat140-169, hu
PSMArat281-284, huPSMArat300-344, hu PSMArat683-690 and
huPSMArat716-750. As furthermore shown in FIG. 20 there is a lack
of binding for PSMA-P7 HL.times.I2C HL to the construct
huPSMArat598-617, which demonstrates the presence of its binding
epitope in the region of amino acids 598 to 617 of human PSMA.
[0693] As shown in Table 1 the amino acids 598 to 617 constitute a
membrane proximal epitope as defined herein. In conclusion the
results of the mapping based on chimeric PSMA constructs
demonstrate that bispecific single-chain antibody PSMA-P7
HL.times.I2C HL recognizes a membrane-proximal target epitope of
human PSMA with <60 .ANG. membrane-distance as defined
herein.
10.3 Epitope Mapping of the PSMA- and CD3-Reactive Bispecific
Single Chain Antibody Molecule PSMA-D4 HL.times.I2C HL
[0694] A PSMA-epitope with 60 .ANG. membrane-distance of bispecific
single chain antibody PSMA-D4 HL.times.I2C HL was confirmed by
epitope mapping using a peptide scanning approach. Peptide scanning
uses overlapping peptides of a given protein and analyses antibody
binding to immobilized peptides by enzyme-linked immunosorbent
assays (ELISAs). The epitope mapping experiments with the PSMA
bispecific single chain antibody PSMA-D4 HL.times.I2C HL were
performed as described in detail in Bernard et al. 2004, J. Biol.
Chem., 279: 24313-22 and Teeling et al. 2006, J Immunol., 177:
362-71.
[0695] In brief, 693 different 15-mer peptides were synthesized
that span the entire extracellular amino acid sequence of human
PSMA and overlap with each neighboring 15-mer peptide by 14 amino
acids. These peptides were coated to ELISA wells in a 384-well
plate format. For this series of experiments, the anti-PSMA scFv
fragment of bispecific single chain antibody PSMA-D4 HL.times.I2C
HL was produced in E. coli and used for ELISA as crude periplasmic
extracts prepared as described herein. The scFv antibody was
incubated with the peptides and specific binding detected using an
anti-His antibody. Binding signals were measured in a 384-well
ELISA reader. As shown in the FIG. 21 a clear maximum signal was
obtained for a peptide spanning over the amino acids threonine 334
to threonine 339, which demonstrates the presence of binding
epitope of PSMA-D4 HL.times.I2C HL in the region of amino acids 334
to 339 of human PSMA. As shown in Table 1 threonine 334 and
threonine 339 constitute a membrane-distal epitope as defined
herein.
[0696] In conclusion the results of the mapping based on peptide
scanning demonstrate that bispecific single-chain antibody PSMA-D4
HL.times.I2C HL recognizes a membrane-distal target epitope of
human PSMA with 60 .ANG. membrane-distance as defined herein.
10.4 Comparative Analysis of Cytotoxic Activity of Bispecific
Antibodies Single-Chain Antibodies Directed at Membrane-Proximal
and Membrane-Distal Target Epitopes of Human PSMA
[0697] Bioactivity of bispecific single chain antibodies was
analyzed by a CytoTox-Glo.TM. cytotoxicity assay with unstimulated
human PBMC using the CHO cells transfected with human PSMA
described in Example 2.1. As effector cells unstimulated human PBMC
were used.
[0698] Unstimulated human PBMC were obtained as follows:
[0699] Human peripheral blood mononuclear cells (PBMC) were
prepared by Ficoll density gradient centrifugation from enriched
lymphocyte preparations (buffy coats), a side product of blood
banks collecting blood for transfusions. Buffy coats were supplied
by a local blood bank and PBMC were prepared on the same day of
blood collection. After Ficoll density centrifugation and extensive
washes with Dulbecco's PBS (Gibco), remaining erythrocytes were
removed from PBMC via incubation with erythrocyte lysis buffer (155
mM NH4Cl, 10 mM KHCO3, 100 .mu.M EDTA). Platelets were removed via
the supernatant upon centrifugation of PBMC at 100.times.g.
Remaining lymphocytes mainly encompass B and T lymphocytes, NK
cells and monocytes. PBMC were kept in culture at 37.degree. C. and
5% CO2 in RPMI medium (Gibco) with 10% FBS (Gibco). All procedures
were performed according to standard protocols (Current Protocols
in Immunology; Coligan, Kruisbeek, Margulies, Shevach and Strober;
Wiley-Interscience, 2002)
[0700] The CytoTox-Glo.TM. cytotoxicity assay (Kit from Promega)
was used according to the instructions provided by the
manufacturer.
[0701] Each measurement was performed in triplicates with defined
dilution series of purified PSMA specific bispecific antibodies
(0.001 ng/ml to 250 ng/ml) and appropriate controls to define
spontaneous lysis (effector and target cells without bispecific
antibodies) and maximum lysis (addition of detergent digitonin to
cells). 10000/well target and 100000/well effector cells were mixed
in a defined ratio with effector cells in excess (E:T ratio of
10:1). After incubation at 37.degree. C. for 20-24 hours
CytoTox-Glo cytotoxicity assay reagent (AAF-GIo.TM.; part of the
CytoTox-Glo Kit from Promega) was added to all wells. The cells and
the reagent were mixed by orbital shaking and incubated at room
temperature for 1 hour. Determination of the number of dead cells
was performed subsequently by measuring luminescence with a plate
reader (TECAN Spectrafluorometer). The measured signal correlates
directly with the amount of lysed cells.
[0702] On the basis of those measured values the cytotoxicity
values of every individual sample were calculated according to
following formula:
S[%]=(V-B)/(M-B)
[0703] Wherein S is specific toxicity, V is the measured value, B
is the average of blank values and M is the average of maximum
lysis.
[0704] As shown in FIG. 22 the bispecific antibody PSMA-P7
HL.times.I2C HL directed at a membrane-proximal target epitope of
human PSMA (as shown in Example 10.2) demonstrated superior
cytotoxic activity against human PSMA positive target cells as
compared to the bispecific single-chain antibody PSMA-D4
HL.times.I2C HL directed at membrane-distal target epitope of human
PSMA (as shown in Example 10.3).
TABLE-US-00016 TABLE 1 aa distance to aa of pos. HUM RAT reference
(.ANG.) 63 D Q 11.7 79 Q R 35.75 80 I T 37.16 87 E Q 40.16 88 Q H
37.46 91 Q E 33.93 97 Q H 25.2 98 S A 24.96 107 S L 21.07 111 A S
31.1 112 H D 34.65 140 N K 62.43 144 F A 51.27 146 P L 50.14 147 P
S 47.22 154 V I 44.73 157 I V 44.61 161 F Y 48.85 169 M T 62.96 191
D V 68.07 207 K V 46.97 225 V I 56.52 236 A V 45.34 258 I V 46.85
281 R H 50.31 282 G E 52.65 283 I F 52.92 284 A T 55.82 300 Y D
56.23 308 K H 67.6 320 R K 58.61 322 S G 56.59 334 T A 73.45 339 T
K 75.1 344 M L 60.7 349 T Y 52.3 351 E K 48.1 363 R K 15.8 380 S A
35.47 401 S T 11.76 408 E K 7.93 438 N H 31.19 471 Y H 25.5 475 H Y
23.2 482 K P 20.44 495 E D 27.54 498 T K 30.45 499 K E 33.18 504 P
T 38.15 507 S T 35.93 542 E K 42.23 543 T N 42.97 546 F V 43.56 548
G S 39.02 569 M T 28.15 582 G A 14.07 598 R Q 31.22 599 D S 30.9
603 V A 36.05 605 R K 40.9 607 Y H 41.38 609 D E 45.95 610 K T
45.84 613 S N 51.09 617 K N 56.75 624 T A 64.88 626 S M 60.97 627 V
I 57.43 637 K N 42.63 641 E D 38.71 642 I V 36.92 647 S N 29.22 648
E Q 30.75 653 F L 26.85 660 V L 26.27 663 M I 26.27 664 M L 26.99
670 F Y 28.76 683 D G 49.46 690 V I 40.04 716 E N 60.95 717 S N
62.54 721 P T 64.1 726 G R 58.11 733 Y S 49.53 734 V I 46.73 747 S
R 35.94 750 A D 38.19
TABLE-US-00017 TABLE 2 aa distance to aa of pos. HUM MU reference
(.ANG.) 57 F Y 30.42 64 G E 46.67 72 A E 30.96 74 N D 35.61 78 L F
42.46 84 G R 42.58 85 Q E 43.72 88 T I 43.24 93 R S 43.31 101 S T
38.96 102 N D 40.41 136 S Q 55.96 144 N Y 61.64 185 F Y 64.38 186 N
T 63.68 191 K R 57.71 217 N D 58.09 224 A V 56.62 229 T S 60.5 233
V I 54.23 242 E G 49.32 264 I V 59.95 267 I V 63.87 273 A H 70.89
274 Y H 72.78 278 Q M 66.9 284 A E 67.3 300 T S 59 301 D S 60.96
328 Q H 72.16 329 T A 69.98 331 D E 68.26 335 T N 67.63 339 I V
59.27 356 V A 50.4 359 Y Q 56.3 362 I T 60.49 399 N Y 41.15 417 E G
35.94 431 S N 56.56 432 Y S 57.15 457 D Y 47.06 458 Y K 48.96 471 I
L 19.07 486 K Q 33.08 487 I V 29.68 497 A S 11.55 499 K R 7.95 506
E V 18.65 512 E K 37.64 513 V D 39.8 514 D G 43.57 515 E G 44.32
516 I L 41.48 518 L F 34.87 550 R K 27.19 559 S T 15.7 567 M I
19.02 584 L F 42.67 586 Y H 46.36 601 I L 36.05 616 K E 31.12 659 V
I 49.32 661 T S 47.68 736 L I 32.18 739 L R 28.95 741 T Q 27.16
Sequence CWU 0 SQTB SEQUENCE LISTING The patent application
contains a lengthy "Sequence Listing" section. A copy of the
"Sequence Listing" is available in electronic form from the USPTO
web site
(http://seqdata.uspto.gov/?pageRequest=docDetail&DocID=US20190040133A1).
An electronic copy of the "Sequence Listing" will also be available
from the USPTO upon request and payment of the fee set forth in 37
CFR 1.19(b)(3).
0 SQTB SEQUENCE LISTING The patent application contains a lengthy
"Sequence Listing" section. A copy of the "Sequence Listing" is
available in electronic form from the USPTO web site
(http://seqdata.uspto.gov/?pageRequest=docDetail&DocID=US20190040133A1).
An electronic copy of the "Sequence Listing" will also be available
from the USPTO upon request and payment of the fee set forth in 37
CFR 1.19(b)(3).
* * * * *
References